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I had an IRA account which contained only after tax contributions. That was my only traditional IRA account. Subsequently, I did a Roth conversion to put the whole amount in to my Roth IRA account. Now, after my retirement, if I roll over my pre-tax IRA into another traditional IRA account and do another Roth conversion later this year, I understand that the pro-rata rule will apply. But, I do have a few questions: (1) When the pro-rata rule apply, what is the basis? It seems to be that it will be based on the IRA portfolio at the end of the year. But, due to the earlier Roth conversion, I do not have any money in the IRA account that had my after tax money. So, does it mean, at the end of the year, the IRA portfolio has only pre-tax money and, therefore, every single penny I conversed were taxable? If so, does it mean that my after tax money is being double taxed? (2) I tried to look up information from the web. It is saying I am not double taxed. The IRS only allows the Roth conversion to be done proportional to the assets in the IRA portfolio.  If this is the case, does it mean that some of the amount in the IRA account into which I roll over pre-tax 401k will become after tax? (I do not think the account with the earlier Roth conversion will get some money back.)   Please help answer these questions.  I am really lost.