Are HSA contributions through payroll deduction excluded from Medicare wages? Tax question about W-2 reporting
I'm confused about how HSA contributions are supposed to be reported on W-2s for Medicare wages. From what I understand (and how it worked at my previous employers), HSA contributions and other Section 125 plan deductions should be excluded from Medicare wages. I was going through my wife's W-2 from her job at a state agency and noticed something odd. Her employee HSA contributions aren't included in her federal taxable wages (Box 1), which seems right. But they ARE included in her Medicare wages (Box 5). The only things excluded from Medicare wages are her transit deductions and health insurance premiums. Is this correct? Should HSA contributions be included in Medicare wages or not? This seems different from how my previous employers have handled it, and I'm wondering if her employer made a mistake or if I'm misunderstanding something about how these pre-tax deductions work.
19 comments

Hunter Hampton
This is a common point of confusion! HSA contributions made through a Section 125 cafeteria plan (salary reduction) are indeed excluded from federal income tax wages, Social Security wages, AND Medicare wages. If your wife's employer is including HSA contributions in her Medicare wages (Box 5 of W-2), that appears to be incorrect. HSA contributions made through payroll deduction under a proper Section 125 plan should be excluded from: - Box 1 (Federal income tax wages) - Box 3 (Social Security wages) - Box 5 (Medicare wages) The employer might be making a payroll system error. It's fairly common, especially since some other pre-tax deductions have different rules. For example, 401(k) contributions are excluded from income tax but still included in Medicare wages.
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Libby Hassan
AuthorThanks for confirming! I thought I was going crazy because every other job I've had treated it exactly how you described. So it sounds like her employer might have misconfigured their payroll system? Would this affect her actual Medicare tax withholding too, meaning she probably overpaid?
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Hunter Hampton
Yes, if her HSA contributions were incorrectly included in Box 5 (Medicare wages), she would have overpaid her Medicare tax. The Medicare tax rate is 1.45% of wages, so she would have overpaid 1.45% of whatever her HSA contribution amount was for the year. For example, if she contributed $3,000 to her HSA through payroll deduction, she would have overpaid approximately $43.50 in Medicare tax (3000 × 0.0145). You might want to consider having her contact her employer's payroll department to notify them of this potential error.
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Sofia Peña
After struggling with a similar W-2 issue last year where my employer misreported some pre-tax deductions, I found a really helpful tool called taxr.ai (https://taxr.ai) that analyzes your tax documents and spots these kinds of errors. It actually flagged that my HSA contributions were incorrectly included in my Medicare wages just like your wife's situation. What I liked is that it explained exactly what was wrong and gave me the specific IRS references to take back to my HR department. It saved me from having to do all the research myself or hope the HR person knew what they were talking about. They even have a feature that can generate a letter to send to your employer explaining the error.
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Aaron Boston
Does this actually work with complicated W-2 issues? I've tried other tax software and they never seem to catch these kinds of technical errors. How accurate is it really?
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Sophia Carter
I'm wondering how this is different from just talking to an accountant? Did they charge a lot for this service? Seems like something TurboTax should catch.
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Sofia Peña
It absolutely works with complicated W-2 issues! The tool specifically checks for payroll tax calculation errors including HSA, FSA, and other pre-tax contributions. It caught things my regular tax software missed completely because most tax prep software just accepts whatever numbers are on your W-2 without questioning them. The difference from an accountant is accessibility and specialization. While a good accountant might catch this, many don't focus specifically on payroll tax issues. Regular tax software like TurboTax doesn't validate if your W-2 was prepared correctly - it just uses whatever numbers are on there. This tool specifically looks for errors in how your employer reported things.
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Aaron Boston
I just wanted to follow up and say I tried taxr.ai after seeing this thread. I was skeptical at first, but it actually identified that my employer had been incorrectly including my transit benefits in my Medicare wages for the past two years! The tool generated a detailed explanation with IRS references that I emailed to our payroll department. They acknowledged the error and are issuing a corrected W-2. I'm getting back almost $90 in overpaid Medicare taxes that I wouldn't have known about otherwise.
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Chloe Zhang
If you're having trouble getting your employer to fix this W-2 issue, you might want to try Claimyr (https://claimyr.com). I had a similar situation last year with incorrectly reported HSA contributions, and after weeks of my employer not responding, I needed to talk to someone at the IRS. We all know how impossible it is to get through to the IRS phone lines (I tried for days), but Claimyr got me connected to an actual IRS agent in about 20 minutes. You can see how it works here: https://youtu.be/_kiP6q8DX5c. The agent confirmed the reporting error and explained exactly what forms my employer needed to file to correct it.
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Brandon Parker
Wait, how does this even work? The IRS phone lines are literally always jammed. Are you saying this service somehow jumps the queue? That sounds too good to be true.
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Adriana Cohn
Sorry, but this sounds like a scam. There's no way some third-party service can get you through to the IRS faster than calling directly. The IRS doesn't give special access to anyone. I've been a tax preparer for years and we all have to wait on hold just like everyone else.
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Chloe Zhang
It doesn't jump the queue - it waits on hold for you. Their system repeatedly calls and navigates the phone tree until it gets through to an agent. When an agent answers, it calls you and connects you directly to them. No magic, just technology saving you from having to sit on hold for hours. The service works by using automated systems to continuously call the IRS, navigate through all the prompts, and wait on hold so you don't have to. When they finally reach a human agent, they immediately connect you. It's basically like having someone else wait on hold for you.
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Adriana Cohn
I need to apologize and correct myself. After calling the IRS for 3 hours yesterday and getting nowhere, I decided to try Claimyr out of desperation. I was completely wrong - the service actually works exactly as described. Got connected to an IRS agent in about 35 minutes while I was cooking dinner. The agent confirmed that HSA contributions through a Section 125 plan should absolutely be excluded from Medicare wages and explained how to request a W-2c from my employer. Sorry for being so skeptical earlier!
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Jace Caspullo
If your employer won't correct the W-2, you can file Form 8275 "Disclosure Statement" with your tax return to explain the discrepancy. You would calculate and pay the correct amount of tax (as if the HSA contribution was properly excluded from Medicare wages) and attach the form explaining why your tax calculation doesn't match the W-2. This lets you pay the correct amount without waiting for a corrected W-2, and it also documents your position in case of questions later.
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Melody Miles
Wouldn't this trigger an audit though? I've always heard that filing anything that doesn't match your W-2 exactly is like waving a red flag at the IRS.
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Jace Caspullo
Filing Form 8275 doesn't automatically trigger an audit. It's actually designed to reduce the risk of penalties by showing you're being transparent about why there's a discrepancy. The IRS appreciates when taxpayers document their positions rather than filing returns with unexplained differences. In this specific case, you would report the W-2 Medicare wages as they appear on your actual W-2, but then you would make an adjustment on Schedule 8812 to reduce the Medicare tax base by the amount of the HSA contribution. The form 8275 explains this adjustment with reference to the relevant tax code sections that confirm HSA contributions are exempt from Medicare tax.
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Nathaniel Mikhaylov
For anyone who comes across this later - I work in payroll and this is 100% an employer error. HSA contributions through a Section 125 cafeteria plan are excluded from ALL FICA taxes (both Social Security and Medicare). The confusion sometimes happens because certain pre-tax deductions have different rules: - 401(k)/403(b) contributions: Excluded from income tax but INCLUDED in FICA (Medicare/SS) - HSA contributions: Excluded from income tax AND FICA when made through a Section 125 plan - Health insurance premiums: Excluded from income tax AND FICA - Dependent care FSA: Excluded from income tax AND FICA - Transit benefits: Excluded from income tax AND FICA up to monthly limits
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Eva St. Cyr
This is super helpful! Do you know if there's a time limit for employers to correct W-2s? My employer made this same mistake for 2023 but I just realized it now in April 2025.
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Katherine Ziminski
There's no specific deadline for employers to issue corrected W-2s once they become aware of an error. However, for tax year 2023, you still have time to address this since the statute of limitations for tax returns is generally 3 years from the filing deadline (so until April 2027 for 2023 returns). If your employer won't issue a corrected W-2c voluntarily, you can contact the IRS and they can compel the employer to correct it. You might also want to check if this affected multiple years - payroll system errors often persist until someone catches them. @f0db9d4314a5 might have more insight on the employer correction process from the payroll side.
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