Yes your AGI is reduced by pre-taxed items. Those come out of your paycheck pre-tax meaning before taxes. The amount in your W2 box 1 is already reduced for them so you don't need to enter them in your tax return. You should notice that box 1 is less than boxes 3 & 5 on your W2. That's why we always tell people not to file using your paystubs, the W2 can be different than the gross pay because of the pre-tax items.
