Discussion of our financial instruments’ exposure to market risk. Our discussion of our results of operations, financial condition, and cash flows for Q2 2025 and YTD 2025 can be found in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” within our filing of Form 10-Q for the fiscal quarter ended June 29, 2025. This MD&A discussion contains forward-looking statements that involve risks and uncertainties. See Consideration Regarding Forward-Looking Statements preceding the Condensed Consolidated Financial Statements section of this report for additional factors relating to such statements. This MD&A should be read in conjunction with our condensed consolidated financial statements and accompanying notes included in this report and our Annual Report on Form 10-K for the fiscal year ended December 28, 2025. Operating results are not necessarily indicative of results that may occur in future periods. MANAGEMENT’S OVERVIEW AND OUTLOOK This overview and outlook provide a high-level discussion of our operating results and significant known trends that affect our business. We believe an understanding of these trends is important to understanding our financial results for the periods being reported herein as well as our future financial performance. This summary is not intended to be exhaustive, nor is it intended to be a substitute for the detailed discussion and analysis provided elsewhere. About Illumina Our focus on innovation has established us as a global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture and other emerging segments. Our customers include leading genomic research centers, academic institutions, government laboratories, and hospitals, as well as pharmaceutical, biotechnology, commercial molecular diagnostic laboratories, and consumer genomics companies. Our comprehensive line of products addresses the scale of experimentation and breadth of functional analysis to advance disease research, drug development, and the development of molecular tests. This portfolio of leading-edge sequencing and array-based solutions addresses a range of genomic complexity and throughput, enabling researchers and clinical practitioners to select the best solution for their scientific challenge. 30 Table of Contents On January 30, 2026, we acquired SomaLogic, a proteomics company that provides high-throughput protein measurement technology and related data analysis services, and other specified assets from Standard BioTools. We believe our acquisition of SomaLogic will enhance our presence in the proteomics market and advance our multiomics strategy. We have included the financial results of SomaLogic in our condensed consolidated financial statements from the date of acquisition. Refer to note 2. Acquisitions, Intangible Assets and Goodwill for details. Our financial results have been, and will continue to be, impacted by several significant trends, which are described below. While these trends are important to understanding and evaluating our financial results, this discussion should be read in conjunction with our condensed consolidated financial statements and the notes thereto within the Condensed Consolidated Financial Statements section of this report, and the other transactions, events, and trends discussed in Risk Factors within the Other Key Information section of this report. Financial Overview In 2024, we outlined key strategic goals focused on a return to revenue growth and improved margin performance by the end of 2027. We continued to make progress toward these goals in YTD 2026. Revenue increased 7% to $2,251 million and operating margin increased to 20.2% in YTD 2026 as compared to 18.0% in YTD 2025. Throughout 2025 and 2026, we experienced several headwinds, including macroeconomic factors such as tariffs, inflation, exchange rate fluctuations and concerns about an economic downturn, competitive challenges in our China region, inclusion on the unreliable entities list by regulatory authorities in China, impacts from armed conflicts between Russia and Ukraine and in the Middle East, including Iran, and reductions in the U.S. government’s funding of the NIH. Moreover, in 2026, we have experienced higher fuel, energy, and shipping costs related to the conflict and instability in the Middle East and higher costs associated with memory chips used in our products, both of which have negatively impacted gross margin in 2026. We expect these factors to continue to impact our sales and results of operations in 2026, and beyond, the magnitude and duration of which remains uncertain. In April 2025, the U.S. government and several other countries enacted tariffs. Under the current environment, the largest cost impact to us relates to importation from our manufacturing facility in Singapore. The remainder is a mix of importation of parts and sub-assemblies to our manufacturing operations in the U.S. and importation into China. In February 2026, the U.S. Supreme Court held that the International Emergency Economic Powers Act (IEEPA) does not authorize the imposition of tariffs. In March 2026, the U.S. Court of International Trade ordered U.S. Customs and Border Protection (CBP) to process refunds of IEEPA-related tariffs, and CBP has been implementing that process in phases. We have incurred significant costs under IEEPA-related tariffs since their implementation. While we intend to seek refunds, and have begun that process, the timing and amount of recoveries remain uncertain and will depend on the scope and timing of future phases, any further court or administrative developments, and completion of applicable administrative steps. We expect to recognize any recoveries, which to date have been immaterial, in our consolidated financial statements when realized (generally upon receipt). We have taken and will continue to take action to mitigate the impact of tariffs. We have partially mitigated the effects of tariffs through supply-chain optimization, cost measures, and pricing actions, and aim to continue such efforts in the future. Financial highlights for YTD 2026 included the following: •Revenue increased 7% in YTD 2026 to $2,251 million compared to $2,100 million in YTD 2025 primarily due to increases in consumables and instruments related to demand for our NovaSeq X instrument. Service and other revenue increased primarily due to revenue attributable to SomaLogic, which we acquired in January 2026. •Gross margin was 66.2% in YTD 2026 compared to 65.6% in YTD 2025. The increase in gross margin was driven primarily by a $23 million intangible asset impairment recognized in Q2 2025. Excluding this impact, gross margin decreased primarily due to higher tariff costs, increased sales mix toward lower-margin instruments as compared to higher-margin consumables, the addition of lower-margin SomaLogic revenue, and higher memory chip and freight costs, partially offset by decreases for field service and warranty costs. Gross margin depends on many factors, including: market conditions that may impact our pricing; sales mix changes among consumables, instruments, services, and strategic partnership revenue; product mix changes between established products and new products; excess and obsolete inventories; royalties; our cost structure for manufacturing operations relative to volume; freight costs; tariffs; and product support obligations. 31 Table of Contents •Income from operations was $454 million in YTD 2026 compared to $378 million in YTD 2025. The increase was due to an increase in gross profit of $113 million, offset by an increase in operating expense of $37 million. The increase in operating expense was primarily due to increases in legal expenses, costs related to our ERP upgrade, and employee-related compensation costs, partially offset by a decrease in restructuring charges of $36 million and an increase in benefits recognized from government incentives of $21 million. •Our effective tax rate was 18.4% in YTD 2026 compared to 25.1% in YTD 2025. The variance from the U.S. federal statutory tax rate of 21% was primarily due to prior year tax return adjustments. The tax rate in YTD 2026 was favorably impacted by the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as in Singapore. •We ended Q2 2026 with cash, cash equivalents, and short-term investments totaling $1,168 million, of which approximately $435 million was held by our foreign subsidiaries. RESULTS OF OPERATIONS To enhance comparability, the following table sets forth unaudited condensed consolidated statement of operations data for the specified reporting periods, stated as a percentage of total revenue.(1) Q2 2026 Q2 2025 YTD 2026 YTD 2025 Revenue: Product revenue 84.7 % 86.1 % 84.4 % 85.4 % Service and other revenue 15.3 13.9 15.6 14.6 Total revenue 100.0 100.0 100.0 100.0 Cost of revenue: Cost of product revenue 25.1 26.1 25.1 25.2 Cost of service and other revenue 6.9 6.7 7.1 7.6 Amortization of acquired intangible assets 1.6 1.6 1.6 1.6 Total cost of revenue 33.6 34.4 33.8 34.4 Gross profit 66.4 65.6 66.2 65.6 Operating expense: Research and development 21.7 23.3 21.8 23.8 Selling, general and administrative 23.6 22.1 24.2 23.8 Total operating expense 45.3 45.4 46.0 47.6 Income from operations 21.1 20.2 20.2 18.0 Other income (expense): Interest income 0.7 0.9 0.8 1.0 Interest expense (2.1) (2.4) (2.1) (2.4) Other income (expense), net 2.7 10.2 (0.3) 6.6 Total other income (expense), net 1.3 8.7 (1.6) 5.2 Income before income taxes 22.4 28.9 18.6 23.2 Provision for income taxes 4.6 6.7 3.4 5.8 Net income 17.8 % 22.2 % 15.2 % 17.4 % _____________ (1)Percentages may not recalculate due to rounding. 32 Table of Contents Revenue Dollars in millions Q2 2026 Q2 2025 Change % Change YTD 2026 YTD 2025 Change % Change Consumables $ 852 $ 811 $ 41 5 % $ 1,649 $ 1,580 $ 69 4 % Instruments 130 101 29 29 250 213 37 17 Total product revenue 982 912 70 8 1,899 1,793 106 6 Service and other revenue 177 147 30 20 352 307 45 15 Total revenue $ 1,159 $ 1,059 $ 100 9 % $ 2,251 $ 2,100 $ 151 7 % Consumables revenue increased in Q2 2026 and YTD 2026 primarily due to greater demand for high-throughput consumables, supported by continued growth of the NovaSeq X installed base, partially offset by a decrease in mid-throughput consumables. Instruments revenue increased in Q2 2026 and YTD 2026 primarily driven by higher NovaSeq X and MiSeq i100 shipments. Service and other revenue increased in Q2 2026 and YTD 2026 primarily due to revenue attributable to SomaLogic, which we acquired in January 2026, and increases in revenue from our development and licensing agreements and informatics solutions. Total revenue in Q2 2026 and YTD 2026 was impacted, across all products and services, by a decrease in revenue from our Greater China region of $7 million and $27 million, respectively, primarily due to our inclusion on the unreliable entities list. Gross Margin Dollars in millions Q2 2026 Q2 2025 Change % Change YTD 2026 YTD 2025 Change % Change Gross profit $ 770 $ 695 $ 75 11 % $ 1,491 $ 1,378 $ 113 8 % Gross margin 66.4 % 65.6 % 66.2 % 65.6 % Gross margin increased in Q2 2026 and YTD 2026 primarily due to a $23 million intangible asset impairment recognized in Q2 2025. Excluding this impact, gross margin decreased in Q2 2026 and YTD 2026. The decrease in Q2 2026 is primarily due to an increased sales mix toward lower-margin instruments as compared to higher-margin consumables, rising memory costs, higher freight costs resulting from the Middle East conflict, and the contribution of lower-margin SomaLogic revenue, partially offset by lower tariff costs as a result of ongoing operational initiatives. The decrease in YTD 2026 is primarily due to higher tariff costs, an increased sales mix toward instruments as compared to consumables, rising memory and higher freight costs, and the addition of SomaLogic revenue, partially offset by decreases in field service and warranty costs. Operating Expense Dollars in millions Q2 2026 Q2 2025 Change % Change YTD 2026 YTD 2025 Change % Change Research and development $ 252 $ 247 $ 5 2 % $ 492 $ 499 $ (7) (1) % Selling, general and administrative 273 234 39 17 545 501 44 9 Total operating expense $ 525 $ 481 $ 44 9 % $ 1,037 $ 1,000 $ 37 4 % R&D expense increased in Q2 2026 primarily due to increases in lab supply and employee-related compensation costs, partially offset by a decrease in restructuring charges of $4 million and an increase in government incentive benefits of $3 million. R&D expense decreased in YTD 2026 primarily due to a decrease in restructuring charges of $14 million and an increase in government incentives of $7 million, partially offset by increases in lab supply costs. 33 Table of Contents SG&A expense increased in Q2 2026 and YTD 2026 primarily due to: + increase in employee-related compensation costs + increase in legal expenses related primarily to various IP litigation matters + lower net gain recognized on contingent consideration liabilities in Q2 2026; flat in YTD 2026 + increase in costs associated with the upgrade of our global enterprise resource planning (ERP) system - decrease in restructuring charges of $3 million and $22 million, respectively, for employee severance costs - increase in government incentive benefits of $15 million and $14 million, respectively Other Income (Expense) Dollars in millions Q2 2026 Q2 2025 Change % Change YTD 2026 YTD 2025 Change % Change Interest income $ 8 $ 10 $ (2) (20) % $ 19 $ 21 $ (2) (10) % Interest expense (24) (25) 1 (4) (47) (50) 3 (6) Other income (expense), net 31 107 (76) (71) (9) 139 (148) (106) Total other income (expense), net $ 15 $ 92 $ (77) (84) % $ (37) $ 110 $ (147) (134) % Interest income consisted primarily of interest on our money market funds. Interest expense consisted primarily of interest on our outstanding term debt. The decrease in other income (expense), net in Q2 2026 was primarily due to a comparatively larger gain recognized on our retained GRAIL investment in Q2 2025. The fluctuation in other income (expense), net in YTD 2026 was primarily due to a net loss recognized on our GRAIL investment in YTD 2026, consisting of realized and unrealized activity, compared to a considerable net gain recognized in YTD 2025. Provision for Income Taxes Dollars in millions Q2 2026 Q2 2025 Change % Change YTD 2026 YTD 2025 Change % Change Income before income taxes $ 260 $ 306 $ (46) (15) % $ 417 $ 488 $ (71) (15) % Provision for income taxes 53 71 (18) (25) 77 122 (45) (37) Net income $ 207 $ 235 $ (28) (12) % $ 340 $ 366 $ (26) (7) % Effective tax rate 20.5 % 23.4 % 18.4 % 25.1 % Our effective tax rate was 20.5% and 18.4% in Q2 2026 and YTD 2026, compared to 23.4% and 25.1% in Q2 2025 and YTD 2025, respectively. The variance from the U.S. federal statutory tax rate of 21% for YTD 2026 was primarily due to prior year tax return adjustments. The tax rate in Q2 2026 and YTD 2026 was favorably impacted by the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as in Singapore. In Q2 2025 and YTD 2025, the variance from the U.S. federal statutory tax rate of 21% was primarily due to the $10 million and $20 million income tax expense impact of capitalizing research and development expenses for tax purposes, respectively. The income tax rate in Q2 2025 and YTD 2025 was favorably impacted by the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as in Singapore. Our future effective tax rate may vary from the U.S. federal statutory tax rate due to the mix of earnings in tax jurisdictions with different statutory tax rates and the other factors discussed in the risk factor “We are subject to risks related to taxation in multiple jurisdictions” described in “Risk Factors” within the Business & Market Information section of our Annual Report on Form 10-K for the fiscal year ended December 28, 2025. 34 Table of Contents LIQUIDITY AND CAPITAL RESOURCES As of June 28, 2026, we had $1,040 million in cash and cash equivalents, of which $435 million was held by foreign subsidiaries. Cash and cash equivalents decreased by $378 million from December 28, 2025 due to factors described in the “Cash Flow Summary” below. Our primary source of liquidity, other than our holdings of cash, cash equivalents, and investments, has been cash flows from operations and, from time to time, issuances of debt. Our ability to generate cash from operations, supplemented with the issuance of debt and/or liquidation of our short-term investments, provides us with the financial flexibility we need to meet operating, investing, and financing needs. In YTD 2026, we received proceeds from sales of our short-term investment in GRAIL of $104 million. As of June 28, 2026, we had $128 million remaining in short-term investments, primarily comprised of marketable equity securities. On January 30, 2026, we acquired SomaLogic for a total purchase price of $460 million, including cash of $382 million and contingent consideration with an estimated fair value of $81 million, offset by $3 million for the settlement of a preexisting relationship. Under the contingent consideration arrangements, Standard BioTools is eligible to receive up to $75 million in milestone payments, comprised of up to $25 million based on 2025 performance and up to $50 million based on 2026 performance, due upon the achievement of specified revenue targets. In Q2 2026, we paid $25 million for the milestone payment earned for the 2025 performance period. Standard BioTools is also entitled to receive a 2% royalty on revenues generated from sales of SOMAmer-based NGS library preparation kits, paid quarterly for 10 years through January 2036. As of June 28, 2026, the aggregate fair value of our remaining contingent consideration liabilities was $37 million, included in accrued liabilities. On July 27, 2026, we paid $30 million to buyout the remaining obligations that were outstanding as of June 28, 2026. In November 2025, we issued $500 million aggregate principal amount of 2030 Term Notes, which mature on December 12, 2030 and accrue interest at a rate of 4.750% per annum, payable semi-annually in June and December of each year. In September 2024, we issued $500 million aggregate principal amount of 2026 Term Notes, which mature on September 9, 2026 and accrue interest at a rate of 4.650% per annum, payable semi-annually in March and September of each year. In December 2022, we issued $500 million aggregate principal amount of 2027 Term Notes, which mature on December 13, 2027 and accrue interest at a rate of 5.750% per annum, payable semi-annually in June and December of each year. In March 2021, we issued $500 million aggregate principal amount of 2031 Term Notes, which mature on March 23, 2031 and accrue interest at a rate of 2.550% per annum, payable semi-annually in March and September of each year. We may redeem for cash all or any portion of the 2026, 2027, 2030, or 2031 Term Notes, at our option, at any time prior to maturity. In January 2023, we entered into the Revolving Credit Agreement, which provides us with a $750 million senior unsecured five-year revolving credit facility, including a $40 million sublimit for swingline borrowings and a $50 million sublimit for letters of credit. The credit facility matures, and all amounts outstanding become due and payable in full, on January 4, 2028, subject to two one-year extensions at our option, the consent of the extending lenders, and satisfaction of certain other conditions. As of June 28, 2026, there were no outstanding borrowings. As of June 28, 2026, the fair value of our contingent consideration liability related to GRAIL was $40 million, of which $39 million was included in other long-term liabilities. The contingent value rights entitle the holders to receive future cash payments on a quarterly basis (Covered Revenue Payments) representing a pro rata portion of certain GRAIL-related revenues (Covered Revenues) each year through August 2033. This reflects a 2.5% payment right to the first $1 billion of revenue each year for 12 years. Revenue above $1 billion each year is subject to a 9% contingent payment right during this same period. In YTD 2026, we paid $794,000 in aggregate Covered Revenue Payments related to aggregate Covered Revenues for the period Q4 2025 through Q1 2026 of $84 million. In August 2024, our Board of Directors authorized the 2024 Repurchase Program, which canceled and superseded all prior and available repurchase authorizations, to repurchase up to $1.5 billion of our outstanding common stock. In April 2026, our Board of Directors authorized the 2026 Repurchase Program to repurchase up to $1.5 billion of our outstanding common stock. The 2026 Repurchase Program is in addition to the $1.5 billion previously authorized under the 2024 Repurchase Program. Repurchases under both programs may be completed through open market purchases, pursuant to Rule 10b5-1 or Rule 10b-18, or through an accelerated share repurchase program. As of June 28, 2026, authorizations to repurchase up to approximately $279 million and $1.5 billion of our outstanding common stock remained available under the 2024 and 2026 Repurchase Programs, respectively. We intend to continue to repurchase incremental shares over the course of 2026. 35 Table of Contents As of June 28, 2026, we had $3 million, $20 million, and $12 million, respectively, remaining in capital commitments to three investment funds that are callable through December 2027, July 2029, and December 2034, respectively. We anticipate that our current cash, cash equivalents, and short-term investments, together with cash provided by operating activities and available borrowing capacity under the Revolving Credit Facility, are sufficient to fund our near-term capital and operating needs for at least the next 12 months. Operating needs include the planned costs to operate our business, including amounts required to fund working capital and capital expenditures. Our primary short-term needs for capital, which are subject to change, may include: •support of commercialization efforts related to our current and future products; •acquisitions of equipment and other fixed assets for use in our current and future manufacturing and research and development facilities; •the continued advancement of research and development efforts; •potential strategic acquisitions and investments; •repayment of debt obligations; •repurchases of our outstanding common stock; and •the evolving needs of our facilities, including costs of leasing and building out facilities. We expect that our revenue and results of operations, as well as the status of each of our new product development programs, will significantly impact our cash management decisions. Our future capital requirements and the adequacy of our available funds will depend on many factors, including: •our ability to successfully commercialize and further develop our technologies and create innovative products in our markets; •scientific progress in our research and development programs and the magnitude of those programs; •competing technological and market developments; and •the need to enter into collaborations with other companies or acquire other companies or technologies to enhance or complement our product and service offerings. Cash Flow Summary In millions YTD 2026 YTD 2025 Net cash provided by operating activities $ 490 $ 474 Net cash used in investing activities (488) (112) Net cash used in financing activities (380) (566) Effect of exchange rate changes on cash and cash equivalents — 11 Net decrease in cash and cash equivalents $ (378) $ (193) Operating Activities Net cash provided by operating activities of $490 million in YTD 2026 consisted of net income of $340 million, plus net adjustments of $278 million, less net changes in operating assets and liabilities of $128 million. The primary adjustments to net income included depreciation and amortization expense of $139 million, share-based compensation expense of $133 million, deferred income taxes of $18 million, and a net loss on investments of $16 million, partially offset by changes in the fair value of contingent consideration liabilities of $32 million. Cash flow impacts from changes in operating assets and liabilities were primarily driven by an increase in other assets, a decrease in other long-term liabilities, an increase in inventory, and a decrease in accrued liabilities, partially offset by a decrease in accounts receivable. 36 Table of Contents Investing Activities Net cash used in investing activities was $488 million in YTD 2026. We paid $417 million for acquisitions and intangible assets, net of cash acquired, invested $78 million in capital expenditures, primarily associated with investments in facilities, and paid $25 million for contingent consideration for the SomaLogic acquisition. We received proceeds from net sales of investments of $32 million, primarily related to sales of our GRAIL investment. Financing Activities Net cash used in financing activities was $380 million in YTD 2026. We used $370 million to repurchase our common stock, inclusive of excise taxes paid, and $33 million to pay taxes related to net share settlement of equity awards. We received proceeds from the sale of shares under our employee stock purchase plan of $24 million. CRITICAL ACCOUNTING POLICIES AND ESTIMATES In preparing our condensed consolidated financial statements, we make estimates, assumptions and judgments that can have a significant impact on our net revenue, operating income, and net income, as well as on the value of certain assets and liabilities on our balance sheet. We believe the estimates, assumptions and judgments involved in the accounting policies described in “Critical Accounting Policies and Estimates” within the Management’s Discussion & Analysis section of our Annual Report on Form 10-K for the fiscal year ended December 28, 2025 have the greatest potential impact on our financial statements, so we consider them to be our critical accounting policies and estimates. Although tariffs, reductions in the U.S. government’s funding of the NIH, our inclusion on the unreliable entities list by regulatory authorities in China, impacts from armed conflicts, including recent conflict in the Middle East and Iran, and macroeconomic factors, such as inflation, exchange rate fluctuations, supply-chain disruptions, and concerns about an economic downturn continue to create additional uncertainty, we continue to use the best information available to inform our critical accounting estimates. There were no material changes to our critical accounting policies and estimates during YTD 2026. RECENT ACCOUNTING PRONOUNCEMENTS For a summary of recent accounting pronouncements applicable to our condensed consolidated financial statements, see note 1. Organization and Significant Accounting Policies within the Condensed Consolidated Financial Statements section of this report, which is incorporated herein by reference. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK There were no substantial changes to our market risks in YTD 2026, when compared to the disclosures in “Quantitative and Qualitative Disclosures about Market Risk” within the Management’s Discussion & Analysis section of our Annual Report on Form 10-K for the fiscal year ended December 28, 2025. OTHER KEY INFORMATION