Your health insurance premiums will be treated in a very similar way to your HSA contributions - added to your box 1 Wages, but deducted from box 3 and box 5 Wages.
"Health and accident insurance premiums paid on behalf of a greater than 2-percent S corporation shareholder-employee are deductible by the S corporation and reportable as wages on the shareholder-employee’s Form W-2, subject to income tax withholding.
However, these additional wages are not subject to Social Security, or Medicare (FICA), or Unemployment (FUTA) taxes if the payments of premiums are made to or on behalf of an employee under a plan or system that makes provision for all or a class of employees (or employees and their dependents). Therefore, the additional compensation is included in the shareholder-employee’s Box 1 (Wages) of Form W-2, Wage and Tax Statement, but is not included in Boxes 3 and 5 of Form W-2.
2-percent shareholder-employee is eligible for an above-the-line deduction in arriving at Adjusted Gross Income (AGI) for amounts paid during the year for medical care premiums if the medical care coverage was established by the S corporation and the shareholder met the other self-employed medical insurance deduction requirements."
See <a rel="nofollow" target="_blank" href="
https://www.irs.gov/businesses/small-businesses-self-employed/s-corporation-compensation-and-medical...>
You deduct this amount as an "above-the line deduction" on line 29 on page 1 of the 1040 - see the instructions for line 29 on page 32 at <a rel="nofollow" target="_blank" href="
https://www.irs.gov/pub/irs-pdf/i1040gi.pdf">https://www.irs.gov/pub/irs-pdf/i1040gi.pdf</a>.
