I believe uncle same usually goes by the FIFO policy (first in first out) so if you sell part of your position, they tax it assuming you are selling the earliest purchases you made in that stock. But you can also elect to identify which stock you are purchasing. If you are selling out of your position...that's a good question that I will need an answer to myself come next fleecing season. Personally, I use quicken so am expecting turbotax to do all of the work for me. Otherwise, I dont' know if you can simply average your gain/loss or not. Of course, you will have to make seperate calculations depending for stock purchases based on capital gains obligations.