Three different dimers of the adenine–thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the NN and NO hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the NN bridge than for the NO one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.