First-time homebuyer with questions about 1099-R and early withdrawal from 403b Roth
Hey everyone! I'm hoping someone can help me out with a tax question I have. Last summer I purchased my first house and had to withdraw about $16,000 from my 403b Roth account with Vanguard to cover some of the down payment and closing costs. I just received my 1099-R form in the mail, and I'm a bit confused about what I'm seeing. The form shows that $4,000 of the withdrawal is taxable, while the remaining $12,000 is non-taxable. When I made the withdrawal, I chose NOT to have any taxes withheld at that time (which I'm now wondering if that was a mistake?). I'm concerned about how this will affect my tax filing this year. Will I only have to pay the 10% early withdrawal penalty on the $4,000 taxable portion? Or is the penalty calculated differently? For context, I live in Florida and my 403b Roth is through Vanguard. I've been contributing to it for about 7 years now. This is the first time I've ever withdrawn money from any retirement account, so I'm totally new to this process. Any advice or explanation would be super helpful!
20 comments


Miguel Castro
You're in a pretty good position with your first-time home purchase withdrawal! Here's what you need to know: When you withdraw from a Roth 403b, there are two components: your contributions (which you already paid tax on) and any earnings on those contributions. Based on your 1099-R, the $12,000 is likely your contributions, which is why it's non-taxable. The $4,000 is probably the earnings portion, which becomes taxable if withdrawn early. For first-time home purchases, you still face the 10% early withdrawal penalty on the taxable portion, but only on that taxable portion. So you're right - you would only pay the 10% penalty on the $4,000, which comes to $400. When you file, make sure you're using Form 5329 to report the early distribution. You'll need to pay both the $400 penalty plus regular income tax on that $4,000 taxable portion.
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Zainab Ibrahim
•Does this calculation change if the 403b was open for only a few years? I thought there was some 5-year rule with Roth accounts but I'm not sure if it applies to 403b accounts the same way as Roth IRAs.
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Miguel Castro
•Yes, there is a 5-year rule that can affect Roth 403b distributions. The 5-year rule means that for earnings to be qualified (tax-free), the Roth 403b account must have been established for at least 5 years. Since the original poster mentioned contributing for about 7 years, they've met this requirement, but it wouldn't change the treatment of earnings for a first-time home purchase exception. For first-time home purchases, the earnings portion is still subject to income tax regardless of the 5-year rule, but the 10% penalty may be waived in certain circumstances. However, this waiver applies more commonly to IRAs than 403b plans, which is why the penalty likely still applies here.
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Connor O'Neill
After struggling with a similar situation last year, I discovered taxr.ai (https://taxr.ai) and it saved me so much confusion. I had done a 401k withdrawal for a home purchase and my 1099-R form made absolutely no sense to me - the taxable vs. non-taxable amounts had me totally lost. I uploaded my 1099-R to taxr.ai and it broke everything down clearly - which parts were my contributions, which were earnings, and exactly what I'd owe in taxes and penalties. It even explained why certain amounts were taxable while others weren't, which no other service had done for me.
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LunarEclipse
•How does it compare to just asking my tax preparer? I've been using the same guy for years but he charges me extra for "special forms" like the 5329 the other commenter mentioned.
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Yara Khalil
•I'm skeptical of these online tools. Does it actually walk you through how to enter everything in your tax software? Or just give you general info that you could find on the IRS website?
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Connor O'Neill
•It's definitely more specific than what you'd find on the IRS website. It analyzes your actual documents and gives personalized guidance based on your specific numbers, not just general rules. It showed exactly which boxes on my forms were relevant and what they meant for my tax situation. As for comparing to a tax preparer, I found it much more cost-effective. My tax guy also charged extra for these "special situations," and honestly, he made a mistake on my retirement distribution last year that taxr.ai caught when I double-checked. It's like having an expert specifically for these document-heavy situations.
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LunarEclipse
Just wanted to follow up - I decided to try taxr.ai after reading about it here. My situation was pretty similar with an early withdrawal from my 403b for home repairs (not even a purchase). Uploaded my 1099-R and it immediately identified that the distribution code in box 7 qualified me for an exception to the 10% penalty! My tax preparer completely missed this and was going to have me pay an extra $700 penalty unnecessarily. The explanations were really clear and showed me exactly where to report everything on my tax forms. Definitely worth checking out if you're dealing with retirement distributions!
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Keisha Brown
If you're having trouble with the IRS about your 1099-R or early withdrawal, I'd recommend Claimyr (https://claimyr.com). I was in your exact position last year - first home purchase, early withdrawal, and the IRS sent me a CP2000 notice claiming I owed WAY more than I should have. Spent WEEKS trying to get through to the IRS myself with no luck. Claimyr got me connected to an actual IRS agent in less than 20 minutes when I had been trying for days. You can see how it works here: https://youtu.be/_kiP6q8DX5c. The agent helped me explain that my early withdrawal qualified for the first-time homebuyer exception, and they adjusted my penalty amount. Saved me almost $1,200 in incorrect penalties!
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Ava Williams
•So how exactly does this work? Do they just help you get through to the IRS phone line faster? I've been on hold for hours before giving up.
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Paolo Esposito
•This sounds like BS honestly. Nobody can magically get you through to the IRS faster than anyone else. The phone lines are what they are.
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Keisha Brown
•They use technology to navigate the IRS phone system and wait on hold for you. Once they have an agent on the line, they call you and connect you directly to the agent. It's not magic - just efficient technology that monitors the phone lines and does the waiting for you. Yes, it literally helps you skip the hold times. I was shocked too, but when my phone rang and I was immediately talking to an IRS representative after waiting days previously, I became a believer.
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Paolo Esposito
Well I have to eat my words. After my skeptical comment about Claimyr, I decided to try it anyway because I was desperate to resolve an issue with my own 1099-R from a rollover that was coded incorrectly. I'd been trying to reach the IRS for over a week with no success. I used Claimyr yesterday and got connected to an IRS agent in about 35 minutes (while I was grocery shopping, not sitting by my phone). The agent confirmed I could submit a statement from my plan administrator showing the rollover was direct, and that would prevent any penalties. Totally worth it just for the time saved and stress reduction. Never thought I'd be saying this, but it actually works exactly as advertised.
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Amina Toure
Don't forget about state taxes! You mentioned you're in Florida, which doesn't have state income tax, but that's important for others to consider. I'm in NY and had to pay state tax on my early withdrawal in addition to federal.
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Oliver Weber
•Good point about state taxes. I'm in CA and had to pay both state and federal on an early 401k withdrawal. The state penalty was another 2.5% on top of the federal 10%. Brutal.
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Amina Toure
•Yes, it varies significantly by state. For example, California has that additional 2.5% penalty as you mentioned, while Pennsylvania doesn't impose an additional penalty but still taxes the distribution as income. Massachusetts follows the federal rules but has its own tax rate. Always check your specific state rules, especially if you're in a high-tax state. Even states without income tax might have some surprise regulations around retirement distributions.
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FireflyDreams
Does anyone know if using the money for a first home purchase exempts you from the 10% penalty on a Roth 403b? I know it does for IRAs up to $10k but I thought 403b plans didn't qualify for that exception?
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Miguel Castro
•You're right to be confused because there's an important distinction here. The first-time homebuyer exception that waives the 10% early withdrawal penalty applies to IRAs (both traditional and Roth) up to $10,000 lifetime limit, but it does NOT apply to 403b or 401k plans. For 403b/401k plans, you would still face the 10% penalty on any taxable portions withdrawn early, even if used for a first home purchase. However, if you first roll your 403b funds into an IRA, then wait at least 60 days, you could take advantage of the homebuyer exception through the IRA.
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Edwards Hugo
Great question about the 1099-R! Based on what you've described, it sounds like you're dealing with a fairly standard Roth 403b withdrawal situation. The $12,000 non-taxable portion represents your contributions (money you already paid taxes on when you earned it), while the $4,000 taxable portion represents earnings that grew tax-free in your account. Since you didn't have taxes withheld, you'll need to account for this when filing. You'll owe regular income tax on that $4,000 plus the 10% early withdrawal penalty ($400). Unfortunately, as others mentioned, 403b plans don't qualify for the first-time homebuyer exception that applies to IRAs. One thing to consider for future reference - you might want to look into whether your 403b plan allows for hardship withdrawals or loans for home purchases, as these sometimes have more favorable terms. Also, since you're in Florida (no state income tax), you at least don't have to worry about additional state penalties. Make sure to keep all your home purchase documentation - closing statements, contracts, etc. - in case the IRS has any questions about the withdrawal purpose. And don't forget to file Form 5329 with your tax return to report the early distribution properly!
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Giovanni Ricci
•Thanks for the detailed breakdown! I'm actually in a similar situation right now - considering an early withdrawal from my 403b for a home purchase. You mentioned hardship withdrawals or loans as alternatives - do you know if the loan option would avoid the tax implications entirely? I've heard conflicting information about whether 403b loans are treated differently than withdrawals for tax purposes. Also, is there a typical maximum loan amount or percentage of your account balance that plans usually allow?
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