What Is Form 5498-SA and How Does It Affect Your Taxes?

Form 5498-SA is an informational tax form your HSA trustee or custodian sends to you and the IRS each year to report contributions to your Health Savings Account, Archer MSA, or Medicare Advantage MSA.¹ You don’t attach it to your return, and you don’t need it in hand to file. It arrives after tax season and works as a confirmation of the contribution numbers you should already be tracking.

What Each Box on Form 5498-SA Reports

The form has six boxes, and the layout trips people up because Box 1 is not where HSA contributions go. Box 1 is reserved for Archer MSA contributions only. If you have a regular HSA, expect Box 1 to be blank.²

Box 1 shows Archer MSA contributions made during the calendar year and through April 15 of the following year.
Box 2 shows total contributions to your HSA or Archer MSA made during the calendar year, including employer contributions, your own contributions, and any qualified funding distribution transferred from an IRA. Rollovers are not included here.
Box 3 shows contributions deposited in the following year but designated for the reporting tax year. A January 2027 deposit counted toward the 2026 limit lands in Box 3.
Box 4 shows rollover contributions moved from one HSA or Archer MSA into this account during the calendar year.
Box 5 shows the fair market value of the account as of December 31.
Box 6 shows a code identifying the type of account being reported.

The participant instructions printed on the form say Boxes 2 and 3 are “provided for IRS use only.” That doesn’t mean the numbers are irrelevant to you. It means you shouldn’t use the form itself to calculate your deduction. Use your own records, and treat the 5498-SA as a cross-check.²

Why It Arrives After You File

Custodians must send Form 5498-SA by May 31 of the year after the reporting year. If May 31 lands on a weekend or holiday, the deadline shifts to the next business day.³ That’s roughly six weeks after the April filing deadline, which confuses people expecting it alongside their W-2s in January.

The delay is built in on purpose. You can make HSA contributions for the prior tax year up to the April filing deadline, so a contribution deposited on April 10, 2027 and designated for 2026 still counts toward your 2026 limit. The custodian needs time to capture those late contributions in Box 3 before filing.¹

Don’t wait for it. File using your own contribution records. When the form shows up in late May, compare it to what you reported. If it flags a discrepancy, such as an employer deposit you didn’t track or a contribution you forgot, you’ll need to amend. If you’ve been tracking through your custodian’s online portal, the numbers usually match.

How the Numbers Reach Your Tax Return

You never attach Form 5498-SA to your return. The contribution data on it feeds Form 8889, which is the form that actually calculates your HSA deduction and gets filed with your 1040.⁴

Form 8889 does three jobs. It reports total HSA contributions for the year, calculates your allowable deduction, and reports any distributions. The deduction it produces is above-the-line, so it reduces your adjusted gross income whether or not you itemize.⁵

Using Form 5498-SA to Catch Excess Contributions

Contributions above your annual limit are hit with a 6% excise tax for every year they remain in the account. The penalty is calculated on Form 5329, not Form 8889, which is a common point of confusion. Form 8889 helps identify the excess; Form 5329 is where the penalty is computed.⁶

You can avoid the 6% tax by withdrawing the excess before the due date of your return, including extensions. You have to pull both the excess amount and any earnings it generated. You can’t deduct the withdrawn amount, and the earnings become taxable income in the year you withdraw them.⁴

Already filed and then spotted the problem? You get a second chance. Withdraw the excess within six months after the original filing deadline (not counting extensions), then file an amended return with “Filed pursuant to section 301.9100-2” written at the top.⁴

This is where Form 5498-SA earns its keep. When it arrives in late May showing a contribution total that doesn’t match your return, that’s your cue to act before the six-month window closes.

Rollovers in Box 4 (And the Transfer That Doesn’t Show Up)

Box 4 captures rollovers: money that was distributed to you from one HSA or Archer MSA and redeposited into another within 60 days. Rollovers don’t count toward your annual limit and aren’t deductible, which is why they’re broken out from Box 2.² You’re limited to one rollover every 12 months.

A direct trustee-to-trustee transfer is different. The money moves between custodians without passing through your hands. There’s no frequency limit, and the transfer doesn’t appear in Box 4 at all. If you’re changing HSA providers, the direct transfer is almost always the safer path.

Box 2 does include one unusual item: a qualified HSA funding distribution, meaning a trustee-to-trustee transfer from a traditional IRA into your HSA. The tax code allows a one-time transfer of this type up to your annual HSA contribution limit. It counts toward the year’s contribution limit but avoids the income tax you’d normally owe on an IRA withdrawal.³

Form 5498-SA vs. Form 1099-SA

Form 5498-SA reports what goes into the account. Form 1099-SA reports what comes out. If you took any distributions from your HSA during the year, your custodian will issue a 1099-SA showing the gross amount distributed, and it arrives in January or February in time for filing.³

The custodian doesn’t determine whether your distributions were used for qualified medical expenses. That’s your job. On Form 8889, you report the total from the 1099-SA and then indicate how much went to qualified expenses. Anything else becomes taxable income, plus a 20% penalty if you’re under 65.⁴

Archer MSAs and Medicare Advantage MSAs

Form 5498-SA also covers two less common accounts. Archer MSAs, the HSA’s predecessor, can no longer be newly established, but existing accounts still generate 5498-SA filings, and their contributions appear in Box 1 rather than Box 2.² Medicare Advantage MSAs are funded exclusively by Medicare through a high-deductible Medicare Advantage plan; the account holder can’t make personal contributions, and the form is still filed each year to report the year-end fair market value even when no new contributions were made.¹

1
Internal Revenue Service. About Form 5498-SA, HSA, Archer MSA, or Medicare Advantage MSA Information
2
Internal Revenue Service. Form 5498-SA (Rev. December 2026)
3
Internal Revenue Service. Instructions for Forms 1099-SA and 5498-SA
4
Internal Revenue Service. Instructions for Form 8889 (2025)
5
Internal Revenue Service. Publication 969 (2025), Health Savings Accounts and Other Tax-Favored Health Plans
6
Internal Revenue Service. Form 5329, Additional Taxes on Qualified Plans (Including IRAs) and Other Tax-Favored Accounts