I am retiring (age 63) and have a 401K that I have made some after tax contributions to (in addition to before tax contribution), these after tax contributions were invested in company stock (publicly traded). Can I/should I roll these after tax contributions, and the appreciation of the stock, into a Roth IRA?
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See IRS Notice 2014-54 regarding splitting a distribution from a 401(k) that is partly after-tax:
https://www.irs.gov/pub/irs-drop/n-14-54.pdf
However, instead of doing a rollover of company stock you might want to consider NUA treatment if you qualify and the company stock is highly appreciated.
Why would NUA treatment be more advantageous than just rolling the stock to a Roth IRA, if I'm not planning on withdrawing from the Roth IRA for a long time, if ever?
If your company shares in the after-tax sub-account are highly appreciated, the gains will be taxable if you roll the shares in-kind over to a Roth IRA and you would pay ordinary income tax on those gains. NUA treatment allows the gains to instead be taxed at long-term capital gains rates. Depending on your situation, the lower taxes on the gains might outweigh the benefit of future tax-free growth in the Roth IRA. The analysis is beyond what is practical to do via a forum like this one. You would be better off finding a tax advisor with experience in this area.
Perhaps you don't even qualify for distribution of NUA. To qualify for NUA you must make a lump-sum distribution from your 401(k), distributing everything in a single tax year with no distributions in the intervening years between the year of your qualifying event (generally age 59½ or separation from service from the company) and the year of the lump-sum distribution. Other parts could be rolled over to a traditional IRA to continue to defer taxes.
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