The HSA interview in Turbo Tax does not help - W2 Box 12W is $5000 all of which was employee contributions by me. It appears that turbo tax assumes that the employer has subtracted the employees HSA contribution from Boxes 1,3 &5 of the W-2. The only way I can make it work so that I am not taxed on the $5000 that I contributed is to reduce the Boxes 1,3,5 of the W2 by $5000 which would not be appropriate since I would be changing numbers reported to the IRS.
