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Loans · Fannie Mae Selling GuideA seller second mortgage behind a conventional loan: what Fannie Mae allows

Sometimes a seller agrees to carry part of the price as a second mortgage behind the buyer's new first mortgage, or the buyer takes a second loan from another lender. Fannie Mae buys first mortgages on properties with subordinate financing (Selling Guide B2-1.2-04) if the second lien is evidenced by a promissory note, reflected in a recorded mortgage or deed of trust, and clearly subordinate to the first. The lender must disclose the second and its repayment terms to Fannie Mae, the appraiser and the mortgage insurer, and every lien on the property counts in the combined loan-to-value (CLTV). Acceptable seconds have regular payments that at least cover the interest – no negative amortization – and charge a market interest rate. If seller financing carries a rate more than 2% below current standard rates for second mortgages, it is treated as a sales concession and its amount is deducted from the sales price. Unacceptable terms include negative amortization and a balloon or maturity less than five years after the first mortgage's note date unless the second fully amortizes with level payments – though Fannie Mae accepts these when the second is minimal relative to the borrower's assets or credit. A variable-rate second other than a HELOC must keep the payment constant for each 12-month period. An agreement to share future appreciation with a third party isn't allowed unless it qualifies as a Community Seconds loan. Employer seconds have their own, looser rules.

Requirements (B2-1.2-04)

  1. 1. Documented

    A promissory note and a recorded mortgage or deed of trust.

  2. 2. Subordinate

    Clearly behind the Fannie Mae first mortgage.

  3. 3. Disclosed

    To Fannie Mae, the appraiser and the mortgage insurer, with its repayment terms.

  4. 4. Counted

    Every lien on the property counts in the CLTV.

Terms

  1. Acceptable

    Regular payments covering at least the interest; a market interest rate.

  2. Seller below market

    A seller second more than 2% below standard second-mortgage rates is a sales concession deducted from the price.

  3. Not acceptable

    Negative amortization; a balloon within five years unless it fully amortizes – except when the second is minimal.

  4. Variable rate

    Payment constant for each 12 months (HELOCs excepted).

  5. Shared appreciation

    Not allowed with a third party unless it's a Community Seconds loan.

What the TC can do

  • Tell the lender about any seller carry-back as soon as it's negotiated – it changes the CLTV and the appraisal and MI disclosures.
  • Get the second's note and deed of trust drafted early, with the rate and term the lender accepted.
  • Make sure the title company records the second behind the first at closing.

Questions buyers and sellers ask

Can a seller carry a second mortgage with a conventional loan?

Yes, on a Fannie Mae loan, if the second is a recorded, clearly subordinate note at a market rate with payments covering at least the interest and no balloon within five years (Selling Guide B2-1.2-04).

What if the seller's second mortgage has a low interest rate?

If it is more than 2% below current standard rates for second mortgages, Fannie Mae treats it as a sales concession and deducts the amount from the sales price.

Does a second mortgage count in the loan-to-value?

Yes. All subordinate liens on the property count when the lender calculates the combined loan-to-value (CLTV).

Add the second mortgage note and deed of trust as documents on the deal in ClosingCode, so they're tracked until they're signed and recorded.

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Source: Fannie Mae Selling Guide B2-1.2-04, Subordinate Financing (August 6, 2025), read at selling-guide.fanniemae.com on October 26, 2026.

General information, not legal or financial advice. The lender decides eligibility. ClosingCode is software; it is not a lender or law firm. This guide is not a substitute for the advice or services of an attorney.