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Here are some links to a few folks who have researched the UBTI question. It's difficult to find a difinitive answer and I suspect different tax professionals may have different opinions. I have decided to sell at least part of the MLPs I own in my IRA because of this issue. It's not the $1000/yr. that's a problem, it's the opinion of some that as your cost basis decreases, your distributions become UBTI, and when you sell, you also have the issue of UBTI on ordinary gain.

Here's a quote from an article about MLP questions on a site called MLP HINDsight:

"UBTI recapture in an IRA? When you sell an MLP in any account, there is ordinary income recapture. But in an IRA, is there anything such as UBTI recapture? In other words, beyond the annual UBTI tax (assuming you are above the $1,000 threshold) is there some cumulative UBTI tax that is triggered when I sell an MLP I have owned for a long time in an IRA?
•When you sell an MLP in a regular taxable account, the difference between your original purchase price and your adjusted basis (adjusted down for distributions, and up for allocated income) is recaptured at ordinary income tax rates. The difference between your selling price and the original purchase price is taxed at capital gains rates.
•When you sell an MLP in a IRA or otherwise tax-exempt account, the part that would have been considered ordinary income recapture above would be taxed at UBTI’s graduated tax rates (for any amount above $1,000). So, there are two components of UBTI: the annual UBTI that gets allocated each year, and there is the UBTI recapture upon sale."

Some other thought-provoking (or maddeningly frustrating) articles on the apparently quite complicated subject (be sure to scan the comments):

"MLPs and Your IRA: Home at Last" (I suggest reading this one first.)

"Master Limited Partnership: Your IRA Choices"

"Master Limited Partnerships: Planning and the Death Tax"

"Master Limited Partnership and Your K-1"

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