Molecular structures of complexes of adenine with 12, 13, 14, and 16 water molecules were calculated using the B3LYP/6-31G(d) method. The location of water molecules on one side with respect to the adenine mean plane leads to a significant deformation of the nucleobase geometry. It results in unusual changes to the amino group geometry and a slight increase in the nonplanarity of the purine fragment of the title molecule. The formation of N-H...O hydrogen bonds with the participation of an amino group results in a disruption of the relationship between the pyramidality of the nitrogen atom of the amino group and the length of the C-N bond. Because of the specific geometry of the H bonds, a shortening of the C(6)-N(10) bond in the adenine.12H(2)O complex does not entail a flattening of the nitrogen atom as compared to that of isolated adenine. Our data reveal the possibility of the formation of unusual hydrogen bonds in polyhydrated complexes of adenine.