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Greetings, Dtras, and welcome. You wrote:

<<I began a business on March 1, 1999. The business is a Subchapter S Corp
I am the only shareholder and only employee
I issue myself a monthly payroll check from the corporate checking account Payroll taxes and FICA are deposited monthly.
I established a KEOGH using the paired plan (10% money purchase and 15 % profit sharing)

The corporation's net profit for 1999 (AFTER deduction of $72,000 gross salary) is $5,000.
My questions are:
How much money can I contribute to my money purchase account?
How much money can I contribute to my profit sharing account?
Should these contributions be made from my corporate checking account or my personal checking account.?
The instructions in IRS Publication 560 are very unclear in this area. >>

You should check with your tax advisor for a definitive answer. As the sole employee and under a sole proprietorship, you may contribute to the Keogh only to the extent you have a profit for the year. In the money purchase part of the plan
a corporation must make a contribution of 10% under normal circumstances even when there is no profit
. My guess is in this instance you must use all of the $5K for the money purchase contribution, but don't have to put in another $2.5K because you're the only participant as well as the only owner. Like I said, though, see you tax advisor to be sure.

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