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The rules for the deductibility of health insurance for shareholders of an S corporation (who own more than 2% of the corporation) can be a bit tricky. See below for material taken from IRS Publication 535, Business Expenses:
"For more-than-2% shareholders, the policy can be either in the name of the S corporation or in the name of the shareholder. You can either pay the premiums yourself or your S corporation can pay them and report the premium amounts on Form W-2 as wages to be included in your gross income. However, if the policy is in your name and you pay the premiums yourself, the S corporation must reimburse you and report the premium amounts on Form W-2 as wages to be included in your gross income. Otherwise, the insurance plan will not be considered to be established under your business."
In your case, I'm assuming the COBRA policy is in your name. Basically, the S corp. can cut the check for the COBRA payment or the S corp. can reimburse you for making the COBRA payment personally. However, you have to include the amounts of these payments on the W-2 that your S corp. issues you at the end of the year, which basically results in you and the business paying payroll taxes on the amount of the inusrance paid. It would likely be beneficial to consult a CPA to ensure that this is correctly reported on the 2009 W-2 issued to you by your S corp.
I've included the link to IRS Publication 535 below in case you'd like to read any further details. I hope this helps!!