Assume Organization A acts as an IRA custodian. If Organization A or any of its affiliates participate in the underwriting syndicate of an initial public offering (IPO), is Organization A prohibited from offering shares of the IPO to its IRA owners by reason of its participation in the underwriting syndicate. My concern is that the IRA's purchase of shares in the IPO could be considered a prohibited transaction.

I used to work on the IPO team of a brokerage that usually acted as a selling group member (not technically part of the syndicate, although I don't think that has any bearing on your question). Anyway, we used to allocate shares to IRA accounts all the time. Unless there's more to your question than I'm seeing, the fact that the brokerage is also your IRA custodian doesn't make you a prohibited person under the NASD's freeriding and withholding rules--that is, you're still not an employee of the B/D, nor are there any IRA restrictions for holding IPO shares.