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Greetings, Rob, and welcome. You asked:

<<I am self-employeed and currently invest in a SEP IRA. Due to various circumstances, I will not be able to max out my contributions into that account for tax year 2000. My question is, should I set aside $2000 to invest in a separate Roth IRA account, or should I continue to put the $2000 into my SEP (which I will still be below my max. SEP contribution limit)? What are othe pros and cons of each senario?>>

If you are reduced to a nondeductible contribution to an IRA, then assuming you meed the income requirements a contribution to a Roth in virtually a "no brainer." Earnings accumulate tax deferred and will come out untaxed in a Roth. In a SEP or in a traditional IRA, those earnings will be taxed.

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