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Are the commissions one pays to purchase stocks within an IRA account deducted from the $2000 maximum annual contribution?

No, commissions generated by trading inside an IRA have to be paid by funds already inside the IRA, but please check it out for yourself. The government's reference is at
http://www.irs.ustreas.gov/forms_pubs/pubs/p5900104.htm

which says, in part,

Brokers' commissions. Brokers' commissions paid in connection with your traditional IRA are subject to the contribution limit and are not deductible as a miscellaneous deduction on Schedule A (Form 1040).

Trustees' fees. Trustees' administrative fees are not subject to the contribution limit. A trustee's administrative fees that are billed separately and paid in connection with your traditional IRA are deductible. They are deductible (if they are ordinary and necessary) as a miscellaneous deduction on Schedule A (Form 1040). The deduction is subject to the 2%-of-adjusted-gross- income limit.


Unfortunately, that site doesn't seem to have an equally explicit statement that the same holds for ROTH IRA's, but I'll bet it does. (It's easy to find a trustee whose fee is zero.)

Chips, who bets all his retirement money on a long term buy and hold strategy and incurs no commissions in his IRA
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