Form 1099-SA vs. 5498-SA: What’s the Difference?

Form 1099-SA vs. 5498-SA – Health Savings Accounts (HSAs), Archer Medical Savings Accounts (Archer MSAs), and Medicare Advantage MSAs (MA MSAs) offer tax-advantaged ways to save for medical expenses. If you’re an account holder, you’ll likely encounter IRS Forms 1099-SA and 5498-SA during tax season. These forms play crucial roles in reporting distributions and contributions, but they serve distinct purposes. Understanding the difference between Form 1099-SA and Form 5498-SA can help you navigate your tax obligations more effectively, avoid penalties, and maximize your HSA benefits.

In this article, we’ll break down what each form is, their key differences, when you receive them, and how they impact your taxes. Whether you’re new to HSAs or need a refresher, this guide uses the latest information from trusted sources like the IRS to ensure accuracy for the 2026 tax year.

What is Form 1099-SA?

Form 1099-SA, titled “Distributions From an HSA, Archer MSA, or Medicare Advantage MSA,” is used to report any money withdrawn (distributed) from your HSA, Archer MSA, or MA MSA during the tax year. This includes payments made directly to medical providers or reimbursements to you as the account holder. A separate form is required for each type of account.

Key Details on Form 1099-SA

  • Box 1: Gross Distribution – Shows the total amount distributed, including any earnings on excess contributions (but excludes negative amounts or certain returned excess contributions).
  • Box 2: Earnings on Excess Contributions – Reports taxable earnings if excess contributions were withdrawn.
  • Box 3: Distribution Code – Indicates the type of distribution, such as:
    • Code 1: Normal distributions (e.g., for qualified medical expenses).
    • Code 2: Excess contributions removed.
    • Code 3: Disability distributions.
    • Code 4: Death distribution (other than code 6).
    • Code 5: Prohibited transaction.
    • Code 6: Nonspouse beneficiary death distribution after the year of death.
  • Box 4: Fair Market Value (FMV) on Date of Death – Used for death-related distributions.
  • Box 5: Account Type Checkbox – Specifies if it’s an HSA, Archer MSA, or MA MSA.

You won’t receive this form if no distributions occurred in the prior year. Distributions for qualified medical expenses are typically tax-free, but non-qualified ones may be subject to income tax and a 20% penalty.

The trustee or custodian of your account (e.g., your bank or financial institution) files this form with the IRS and sends you a copy by January 31 of the following year.

What is Form 5498-SA?

Form 5498-SA, “HSA, Archer MSA, or Medicare Advantage MSA Information,” reports contributions made to your HSA, Archer MSA, or MA MSA for the tax year. This includes regular contributions, rollovers, and even contributions made in the following year but designated for the prior tax year (up to the tax filing deadline, typically April 15). Like Form 1099-SA, a separate form is filed for each account type.

Key Details on Form 5498-SA

  • Box 1: Archer MSA Contributions – Employee or self-employed contributions to an Archer MSA (gross, including excesses) made in the calendar year and through April 15 of the next year.
  • Box 2: Total Contributions – All HSA or Archer MSA contributions for the calendar year, including qualified HSA funding from IRAs and prior-year contributions.
  • Box 3: Subsequent Year Contributions – Contributions made in the next year but applied to the current tax year.
  • Box 4: Rollover Contributions – Amounts rolled over from another similar account (e.g., Archer MSA to HSA), excluding trustee-to-trustee transfers.
  • Box 5: Fair Market Value (FMV) – The account’s value as of December 31.
  • Box 6: Account Type Checkbox – Indicates HSA, Archer MSA, or MA MSA.

This form is primarily informational and isn’t required for filing your taxes if your contributions are already reported on your W-2 (Box 12, Code W). You won’t receive it if no contributions were made. The trustee or custodian files it with the IRS and provides you a copy by May 31 of the following year.

Key Differences Between Form 1099-SA and 5498-SA

While both forms relate to the same types of accounts (HSAs, Archer MSAs, and MA MSAs), they focus on opposite sides of the transaction: outflows vs. inflows. Here’s a side-by-side comparison:

Aspect Form 1099-SA (Distributions) Form 5498-SA (Contributions)
Primary Purpose Reports withdrawals from the account. Reports deposits into the account, including rollovers.
What It Includes Gross distributions, earnings on excesses, distribution codes, FMV on death. Total contributions, subsequent-year contributions, rollovers, year-end FMV.
When Issued By January 31 if distributions occurred. By May 31, even if contributions extend to April 15 of the next year.
Tax Impact Used to report distributions on IRS Form 8889; non-qualified may be taxable. Informational; contributions often deducted via W-2, but helps verify limits.
Who Files It Trustee/custodian for each distribution type. Trustee/custodian for each account with activity.
If No Activity Not issued if no distributions. Not issued if no contributions or rollovers (and FMV is zero).
Separate Forms Yes, per plan type. Yes, per plan type.

These differences ensure accurate tracking of account activity for tax purposes. For instance, Form 1099-SA helps the IRS monitor if distributions were used for qualified expenses, while Form 5498-SA verifies contribution limits to prevent overfunding.

When and How Do You Receive These Forms?

  • Form 1099-SA: Mailed or electronically delivered by January 31 following the tax year. If you took any distributions, expect it from your account provider (e.g., HSA Bank or HealthEquity). It’s essential for completing IRS Form 8889 on your tax return.
  • Form 5498-SA: Arrives later, by May 31, to account for last-minute contributions. It’s often combined with Form 1099-SA if both apply. Check your online account portal for digital copies.

If you don’t receive them, contact your trustee. Note: These forms aren’t needed if there’s no activity, but always verify with your records.

How Do These Forms Affect Your Taxes?

Both forms feed into IRS Form 8889 (“Health Savings Accounts (HSAs)”), which you attach to your Form 1040.

  • Using Form 1099-SA: Report distributions here. Qualified medical expenses are tax-free, but others are included in income and may incur a 20% penalty (unless you’re 65+, disabled, or it’s a death distribution). Mistaken distributions can be repaid without penalty if done by your tax due date.
  • Using Form 5498-SA: Helps confirm deductible contributions. HSA contributions are tax-deductible (up to annual limits), but excesses trigger a 6% excise tax. Employer contributions are excluded from your income via W-2.

For 2026, HSA contribution limits are typically adjusted for inflation—check the latest IRS guidelines for exact amounts. If you’re dealing with rollovers or death scenarios, consult a tax professional, as rules vary (e.g., surviving spouses may inherit accounts tax-free).

Common Questions About Form 1099-SA vs. 5498-SA

Are Form 1099-SA and 5498-SA the Same?

No—the former tracks outflows (distributions), while the latter tracks inflows (contributions).

Do I Need Form 5498-SA to File Taxes?

Usually not, as it’s informational. Your W-2 often suffices for contribution deductions.

What If I Have Multiple Accounts?

You’ll get separate forms for each, potentially from different providers.

Can I Correct Errors on These Forms?

Yes—contact your trustee for a corrected version if needed.

Conclusion

The difference between Form 1099-SA and 5498-SA boils down to distributions versus contributions, but both are vital for accurate tax reporting on HSAs and similar accounts. By understanding these forms, you can ensure compliance, claim deductions, and avoid unnecessary taxes. Always keep records of your medical expenses and consult IRS resources or a tax advisor for personalized advice, especially with changes in 2026 regulations.

For the most up-to-date information, visit the IRS website or your account provider’s portal. Proper management of these forms can help you make the most of your health savings strategy.