A 1099-SA is an IRS form reporting distributions (withdrawals) from a Health Savings Account, Archer MSA, or Medicare Advantage MSA during the tax year. Your account custodian issues it, listing the gross amount you took out in Box 1 and a code in Box 3 explaining the type of distribution. You use it to complete Form 8889 at tax time.

Why would someone receive a 1099-SA?

You receive a 1099-SA only if you withdrew money from an HSA, Archer MSA, or Medicare Advantage MSA during the year. Spending HSA funds on doctor visits, prescriptions, or other medical costs counts as a distribution, as does correcting an excess contribution or closing the account. No withdrawals means no 1099-SA for that year.

Do I have to report a 1099-SA on my tax return?

Yes. Even when your HSA distributions were entirely for qualified medical expenses and are tax-free, you must report them on Form 8889 filed with your Form 1040. Form 8889 reconciles the Box 1 amount against your qualified expenses, proving how much (if any) is taxable. Skipping it can trigger an IRS notice.

Is a 1099-SA taxable?

Not necessarily. HSA distributions used for qualified medical expenses are tax-free, even though the full amount appears in Box 1. The withdrawal becomes taxable only if you spent it on non-medical expenses, and may face an additional 20% penalty if you're under 65. You report and reconcile this on Form 8889 with your tax return.

What's the difference between a 1099-SA and a 5498-SA?

A 1099-SA reports money taken OUT of your HSA or MSA (distributions), while a 5498-SA reports money put IN (contributions and the year-end fair market value). The custodian issues 1099-SA by the end of January and 5498-SA in May. You need the 1099-SA to complete Form 8889 at tax time.

How long should I keep a 1099-SA?

Keep your 1099-SA at least 7 years with the matching tax return. More importantly, hold the receipts proving each distribution paid a qualified medical expense for as long as the account is open — HSAs let you reimburse yourself years later, and you must be able to substantiate every withdrawal if audited.

Tax

Form 1099-SA

Form 1099-SA is an IRS tax form that reports distributions (withdrawals) you took during the year from a Health Savings Account (HSA), Archer MSA, or Medicare Advantage MSA. The account custodian issues it, showing the gross amount withdrawn and a code explaining why the distribution was made.

Written & maintained by the Granite team · Last updated June 2026

Overview

Form 1099-SA reports money taken OUT of a health savings or medical savings account in a given tax year. It covers HSAs, Archer MSAs, and Medicare Advantage MSAs, listing the gross distribution and a distribution code that tells the IRS the reason for the withdrawal (normal, disability, death, excess-contribution correction, and so on).

It is issued by the account's trustee or custodian (the bank or financial institution holding the account) and sent to you, the account holder, by the end of January following the tax year. You use it to complete Form 8889 and prove your withdrawals went toward qualified medical expenses. Don't confuse it with Form 5498-SA, which reports contributions going IN, or Form 1099-R, which reports retirement-account distributions.

When you’ll get your Form 1099-SA

You paid for medical expenses using your HSA debit card, checks, or reimbursements during the year
You took any withdrawal from an Archer MSA or Medicare Advantage MSA
You corrected an excess contribution by withdrawing it plus earnings
A distribution was made due to disability, death, or a prohibited transaction
You closed or rolled over a health savings account

What’s on your Form 1099-SA

These are the fields Granite reads and extracts automatically the moment you upload one.

Payer (Trustee/Custodian): The bank or financial institution that holds your HSA or MSA and issued the form.
Recipient: The account holder's name and SSN/TIN (the SSN is usually masked).
Box 1 — Gross distribution: The total dollar amount withdrawn from the account during the tax year, including any earnings reported in Box 2.
Box 2 — Earnings on excess contributions: Investment earnings withdrawn alongside an over-contribution you corrected; this portion is taxable.
Box 3 — Distribution code: A single digit explaining the type of distribution: 1=normal, 2=excess contributions, 3=disability, 4=death distribution other than code 6, 5=prohibited transaction, 6=death distribution after the year of death to a nonspouse beneficiary.
Box 4 — Fair market value on date of death: Used only when the account passes to a beneficiary; the account's value as of the holder's death.
Box 5 — Account type: Checkbox indicating whether the account is an HSA, Archer MSA, or MA MSA.

How long to keep it

At least 7 years

Keep each year's 1099-SA with that year's tax return because the IRS can audit HSA distributions for up to 3 years (6 if income was understated). But you also need to prove every withdrawal paid a qualified medical expense — so hold the matching receipts as long as the account stays open, since you can reimburse yourself years later.

How Granite handles your Form 1099-SA

Drop your 1099-SA into Granite and it reads the form automatically — pulling the custodian name, tax year, Box 1 gross distribution, and the distribution code so you never re-key them. It files the form into a 'Tax {year}' collection alongside your other tax documents and links it to the issuing institution as an entity, so searching the custodian or 'HSA distribution' surfaces it instantly. Pair it with the receipts that justify each withdrawal and your audit trail lives in one findable place.

FAQ

Form 1099-SA: common questions

What is a 1099-SA?: A 1099-SA is an IRS form reporting distributions (withdrawals) from a Health Savings Account, Archer MSA, or Medicare Advantage MSA during the tax year. Your account custodian issues it, listing the gross amount you took out in Box 1 and a code in Box 3 explaining the type of distribution. You use it to complete Form 8889 at tax time.
Why would someone receive a 1099-SA?: You receive a 1099-SA only if you withdrew money from an HSA, Archer MSA, or Medicare Advantage MSA during the year. Spending HSA funds on doctor visits, prescriptions, or other medical costs counts as a distribution, as does correcting an excess contribution or closing the account. No withdrawals means no 1099-SA for that year.
Do I have to report a 1099-SA on my tax return?: Yes. Even when your HSA distributions were entirely for qualified medical expenses and are tax-free, you must report them on Form 8889 filed with your Form 1040. Form 8889 reconciles the Box 1 amount against your qualified expenses, proving how much (if any) is taxable. Skipping it can trigger an IRS notice.
Is a 1099-SA taxable?: Not necessarily. HSA distributions used for qualified medical expenses are tax-free, even though the full amount appears in Box 1. The withdrawal becomes taxable only if you spent it on non-medical expenses, and may face an additional 20% penalty if you're under 65. You report and reconcile this on Form 8889 with your tax return.
What's the difference between a 1099-SA and a 5498-SA?: A 1099-SA reports money taken OUT of your HSA or MSA (distributions), while a 5498-SA reports money put IN (contributions and the year-end fair market value). The custodian issues 1099-SA by the end of January and 5498-SA in May. You need the 1099-SA to complete Form 8889 at tax time.
How long should I keep a 1099-SA?: Keep your 1099-SA at least 7 years with the matching tax return. More importantly, hold the receipts proving each distribution paid a qualified medical expense for as long as the account is open — HSAs let you reimburse yourself years later, and you must be able to substantiate every withdrawal if audited.

Sources

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