When dividing an account with after-tax basis pursuant to a QDRO, what happens to the tax basis. Does the QDRO need to, or can the QDRO, specify this? If the QDRO is silent, is the basis split pro-rata? For example, say you have a 50%/50% split and the participant has $8000 in basis. After the split, does the alternate payee have $4000 in basis and the original participant also have $4000 in basis?

That's a pretty good question.
Just my non-lawyer opinion, but it might be hasty to assume a pro-rata split. For example, suppose all the after-tax money was contributed before the marriage, it might not be appropriate to do any split. If possible, the participant might want to consider having the QDRO modified to remove any ambiguity.

Section 72(m) (10)

According to the legislative history of the Retirment Equity Act of 1984, the after tax contributions and attirrbutable income are supposed to be divided up in the same ratio as the division of assets in the plan, e.g., if spouse gets 40% of plan assets the spouse gets 40% of a/t contributions.

The text of IRC section 72(m)(10) is:

"(10)Determination of investment in the contract in the case of qualified domestic relations orders
Under regulations prescribed by the Secretary, in the case of a distribution or payment made to an alternate payee who is the spouse or former spouse of the participant pursuant to a qualified domestic relations order (as defined in section 414(p)), the investment in the contract as of the date prescribed in such regulations shall be allocated on a pro rata basis between the present
value of such distribution or payment and the present value of all other benefits payable with respect to the participant to which such order relates."

Don't know if the IRS has issued any regs (proposed or otherwise) on this section.