Yes, the health insurance premiums you pay may be an AGI deduction
if your S corporation reimburses you for the premiums and includes them in your
W-2 (see below), however the health insurance
paid by your spouse may qualify for an itemized deduction, click here
for the 2016 IRS publication 535, Business Expenses, chapter 6. Insurance, which states: "For
more-than-2% shareholders, a 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 the 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 in box 1 as wages to be included in your gross income. Otherwise,
the insurance plan won’t be considered to be established under your business."
