Avalyn Pharma Inc.

For the period ended Mar 31, 2026. Filed Jun 3, 2026.

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A company's report for each of its first three quarters. The financial statements are not audited. It shows how the business has moved since the last annual report, and what management says changed.

Mar 31, 2026 · Filed Jun 3, 2026

AVLN$29.50+1.2%Stored close · as of Nov 9, 2026

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Contents

Item 6. Exhibits

Furnish the exhibits required by Item 601 of Regulation S-K (§ 229.601 of this chapter).

ExhibitNumber	Description
3.1	Amended and Restated Certificate of Incorporation of Avalyn Pharma Inc. (incorporated by reference to Exhibit 3.1 to the Registrant’s Current Report on Form 8-K (File No. 001-43251).
3.2	Amended and Restated Bylaws of Avalyn Pharma Inc. (incorporated by reference to Exhibit 3.2 to the Registrant’s Current Report on Form 8-K (File No. 001-43251).
4.1†+	Amended and Restated Investors’ Rights Agreement, by and between the Registrant and certain of its stockholders, dated as of April 25, 2025 (incorporated by reference to Exhibit 4.2 to the Registrant’s Registration Statement on Form S-1(File No. 333-294932).
4.2	Form of Common Stock Certificate (incorporated by reference to Exhibit 4.1 to the Registrant's Registration Statement on Form S-1 (File No. 333-294932).
4.3	Warrant to Purchase Stock, dated January 13, 2025, by and between the Registrant and Bruce Montgomery (incorporated by reference to Exhibit 4.3 to the Registrant's Registration Statement on Form S-1 (File No. 333-294932).
4.4+	Warrant to Purchase Stock, dated February 3, 2026, by and between the Registrant and Banc of California (incorporated by reference to Exhibit 4.1 to the Registrant's Registration Statement on Form S-1 (File No. 333-294932).
10.1#	2026 Equity Incentive Plan and form of award agreements thereunder (incorporated by reference to Exhibit 10.3 to the Registrant’s Registration Statement on Form S-1, as amended (File No. 333-294932).
10.2#	2026 Employee Stock Purchase Plan (incorporated by reference to Exhibit 10.4 to the Registrant’s Registration Statement on Form S-1, as amended (File No. 333-294932).
10.3#	Form of Officer Indemnification Agreement, by and between the Registrant and its directors (incorporated by reference to Exhibit 10.5 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294932).
10.4#	Form of Director Indemnification Agreement, by and between the Registrant and its executive officers (incorporated by reference to Exhibit 10.6 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294932).
10.5#	Senior Executive Cash Incentive Bonus Plan (incorporated by reference to Exhibit 10.7 to the Registrant's Registration Statement on Form S-1 (File No. 333-294932).
10.6#	Executive Severance Plan (incorporated by reference to Exhibit 10.8 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.7#	Non-Employee Director Compensation Policy (incorporated by reference to Exhibit 10.9 to the Registrant's Registration Statement on Form S-1 (File No. 333-294932).
10.8#	Compensation Recovery Policy (incorporated by reference to Exhibit 10.10 to the Registrant's Registration Statement on Form S-1 (File No. 333-294932).
10.9*#	Employment Agreement, by and between the Registrant and Lyn Baranowski, effective as of April 29, 2026.
10.10*#	Employment Agreement, by and between the Registrant and Douglas Carlson, effective as of April 29, 2026.
10.11*#	Employment Agreement, by and between the Registrant and Melissa Rhodes, effective as of April 29, 2026.
10.12*#	Employment Agreement, by and between the Registrant and Howard Lazarus, effective as of April 29, 2026.
10.13†+	License Agreement dated April 3, 2017, by and between the Registrant and PARI Technology Services, as amended. (incorporated by reference to Exhibit 10.6 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.14†+	Amendment No. 1 to License Agreement dated October 15, 2020, by and between the Registrant and PARI Technology Services, as amended (incorporated by reference to Exhibit 10.17 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.15†+	Amendment No. 2 to License Agreement dated February 9, 2021, by and between the Registrant and PARI Technology Services, as amended (incorporated by reference to Exhibit 10.18 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.16†+	Material Transfer Agreement, dated January 23, 2020, by and between the Registrant and PARI Technology Services, as amended (incorporated by reference to Exhibit 10.19 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.17†+	Amendment No. 1 to Material Transfer Agreement, dated November 22, 2021, by and between the Registrant and PARI Technology Services, as amended (incorporated by reference to Exhibit 10.20 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.18†+	Amendment No. 2 to Material Transfer Agreement, dated January 22, 2023, by and between the Registrant and PARI Technology Services, as amended (incorporated by reference to Exhibit 10.21 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).

10.19†+	Amendment No. 3 to Material Transfer Agreement, dated March 20, 2025, by and between the Registrant and PARI Technology Services, as amended (incorporated by reference to Exhibit 10.22 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.20†+	Option Agreement, dated January 1, 2024, by and between the Registrant and PARI Technology Services (incorporated by reference to Exhibit 10.23 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.21†+	Sublease Agreement, by and between the Registrant and CRISPR Therapeutics, Inc., dated as of August 29, 2025 (incorporated by reference to Exhibit 10.24 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
10.22†+	Loan and Security Agreement, dated February 3, 2026, by and between the Registrant and Banc of California (incorporated by reference to Exhibit 10.25 to the Registrant’s Registration Statement on Form S-1 (File No. 333-294976).
31.1*	Certification of Principal Executive Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2*	Certification of Principal Financial Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1**	Certification of Principal Executive Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
32.2**	Certification of Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101.INS*	Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document.
101.SCH*	Inline XBRL Taxonomy Extension Schema With Embedded Linkbase Documents
104*	Cover Page Interactive Data File (embedded within the Inline XBRL document)

Filed herewith.

** The certifications furnished in Exhibit 32.1 and 32.2 hereto are deemed to be furnished with this Quarterly Report and will not be deemed to be “filed” for purposes of Section 18 of the Exchange Act, except to the extent that the Registrant specifically incorporates it by reference.

#	Indicates a management contract or any compensatory plan, contract or arrangement.
†	Certain portions of this document that constitute confidential information have been redacted pursuant to Item 601(b)(10) of Regulation S-K.
+	Certain exhibits and schedules to these agreements have been omitted pursuant to Item 601(a)(5) and (6) of Regulation S-K. The registrant will furnish copies of any of the exhibits and schedules to the Securities and Exchange Commission upon request.

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