The pro-rata rule is an important, though commonly misunderstood, rule that affects the taxation of IRA money. It only comes into play when your traditional IRA consists of both pre-tax and after-tax monies. These after-tax dollars can come from non-deductible IRA contributions or rollovers of after-tax funds from employer plans. Either way, once those monies are in the account, subsequent distributions or conversions are subject to the pro-rata rule. The pro-rata rule does not apply to Roth IRA assets. Instead, Roth IRA distributions are subject to their own set of ordering rules.