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☒QUARTERLY REPORT PURSUANT TO SECTION13 OR 15(d)OF THE SECURITIES EXCHANGE ACTOF 1934 For the quarterly period endedMarch 31, 2025OR ☐TRANSITION REPORT PURSUANT TO SECTION13 OR 15(d)OF THE SECURITIES EXCHANGE ACTOF 1934 For the transition period fromtoCommission file number001-38223 RHYTHM PHARMACEUTICALS,INC. (Exact name of registrant as specified in its charter) Securities registered pursuant to Section 12(b) of the Act: Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15 (d) of the Securities Exchange Act of 1934 duringthe preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements forthe past 90 days.Yes☒No☐Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files).Yes☒No☐Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerginggrowth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2of the Exchange Act. Large accelerated filer☒ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new orrevised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐Indicate by check mark whether the registrant is a shell company (as defined in Rule12b-2 of the Exchange Act). Yes☐No☒. The number of shares outstanding of the registrant’s Common Stock as of April 30, 2025 was63,621,472. RHYTHM PHARMACEUTICALS,INC. FORM 10-Q INDEX PageNo. PART IFINANCIAL INFORMATIONItem 1. Condensed Consolidated Financial Statements (Unaudited)3Condensed Consolidated Balance Sheets3Condensed Consolidated Statements of Operations and Comprehensive Loss4Condensed Consolidated Statements of Convertible Preferred Stock andStockholders’ Equity5Condensed Consolidated Statements of Cash Flows6Notesto Unaudited Condensed Consolidated Financial Statements7Item2. Management's Discussion and Analysis of Financial Condition and Results ofOperations26Item3. Quantitative and Qualitative Disclosures About Market Risk39Item4. Controls and Procedures39PARTIIOTHER INFORMATIONItem1. Legal Proceedings40Item 1A. Risk Factors40Item2. Unregistered Sales of Equity Securities and Use of Proceeds103Item 3. Defaults Upon Senior Securities103Item 4. Mine Safety Disclosure104Item 5. Other Information104Item6. Exhibits104SIGNATURES106 PARTI– FINANCIAL INFORMATION Item1.Financial Statements Rhythm Pharmaceuticals, Inc. Condensed Consolidated Balance Sheets (in thousands, except share and per share data) (Unaudited) The accompanying notes are an integral part of these unaudited condensed consolidatedfinancial statements. Rhythm Pharmaceuticals, Inc. Condensed Consolidated Statements of Operations and Comprehensive Loss (in thousands, except share and per share data) (Unaudited) The accompanying notes are an integral part of these unaudited condensed consolidatedfinancial statements. Rhythm Pharmaceuticals, Inc. Condensed Consolidated Statements of Cash Flows (in thousands) (Unaudited) The accompanying notes are an integral part of these unaudited condensed consolidatedfinancial statements. Rhythm Pharmaceuticals,Inc. Notesto Unaudited Condensed Consolidated Financial Statements (In thousands, except share and per share information) 1. Nature of Business Rhythm Pharmaceuticals,Inc. (the “Company” or “we”) is a global, commercial-stagebiopharmaceuticalcompany dedicated to transforming the lives of patients living with rareneuroendocrinediseases.We are focused on advancing our melanocortin-4(MC4R)receptoragonists, including our lead asset, IMCIVREE®(setmelanotide), as a precision medicine designed totreat hyperphagia and severe obesity caused by rare MC4R pathway diseases. While obesity affectshundreds of millions of people worldwide, we are developing therapies for a subset of individualswho have hyperphagia, a pathological insatiable hunger and impaired satiety accompanied bypersistent and abnormal food-seeking behaviors, decreased energy expenditure and severe obesitydue to diseases such as acquired or congenital hypothalamic obesity, Bardet-Biedl syndrome (BBS)or other diseases caused by impaired MC4R pathway signaling. The MC4R pathway is an endocrinepathway in the brain that is responsible for regulating hunger, caloric intake and energy expenditure,which consequently affect body weight. IMCIVREE, an MC4R agonist for which we hold worldwiderights, is the first-ever therapy developed for patients with