Second Amendment to Warrant Certificate

Exhibit 4.2

Second Amendment to Warrant Certificate

This Second Amendment to Warrant Certificate, dated as of May 12, 2025 (this “Amendment”), is entered into by and among Biodesix, Inc. a Delaware corporation (the “Company”) and Perceptive Credit Holdings IV, LP, a Delaware limited partnership (the “Holder”).

Recitals

Whereas, the Company issued to the Holder that certain Warrant Certificate, dated as of November 21, 2022, as amended by that certain First Amendment to Warrant Certificate, dated February 28, 2025, and this Amendment (the “Warrant”). Capitalized terms used herein but not otherwise defined herein shall have the meanings ascribed thereto in the Warrant.

Whereas, following that certain Fifth Amendment to Credit Agreement and Guaranty, dated as of February 28, 2025, by and among the Company, as borrower, the lenders party thereto, and Holder, as administrative agent for the lenders, the Company and the Holder have agreed to amend certain provisions of the Warrant.

Whereas, the Company and the Holder are willing to make such amendments to the Warrant as are further described herein, in accordance with and subject to the terms and conditions of this Amendment.

Now, Therefore, in consideration of the premises and the mutual covenants and the agreements herein set forth, and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto, intending to be legally bound, agree as follows:

(i) On the date hereof (the “Initial Vesting Date”), 3,000,000 Warrant Shares shall become vested and exercisable (such Warrant Shares, the “Initial Warrant Shares”) and shall be exercisable at an Exercise Price equal to $0.4191 (the “Initial Warrant Exercise Price”).

(ii) On the Tranche B Loan Borrowing Date (as defined in the Credit Agreement) (the “Second Tranche Vesting Date”), an additional 1,000,000 Warrant Shares shall become vested and exercisable (such Warrant Shares, the “Second Tranche Warrant Shares”) and shall be exercisable at an Exercise Price equal to $0.4191 (the “Second Tranche Exercise Price”).

(iii) On the Tranche C Loan Borrowing Date (as defined in the Credit Agreement) (the “Third Tranche Vesting Date”), an additional 1,000,000 Warrant Shares shall become vested and exercisable (such Warrant Shares, the “Third Tranche Warrant Shares”) and shall be exercisable at an Exercise Price equal to $0.4191 (the “Third Tranche Exercise Price”).

[Remainder of page intentionally left blank; signatures on following pages]

2

IN WITNESS WHEREOF, the Company and ▇▇▇▇▇▇ have duly executed this Amendment as of the date first written above.

COMPANY: BIODESIX, INC., a Delaware corporation

HOLDER: PERCEPTIVE CREDIT HOLDINGS IV, LP,

a Delaware limited partnership

By: Perceptive Credit Opportunities GP, LLC, its general partner

[Signature Page to Second Amendment to Warrant]