The cooperative contributions to the H-bonding interaction energies of the adenine-thymine and guanine-cytosine base pairs have been evaluated using molecular orbital theory. The energies of the individual bonds in each base pair were ascertained by using models structures that keep one H-bond at a time intact by rotating, one base with respect to the other about the axis of each H-bond to form structures with the bases perpendicular to each other. The energies of the individual H-bonds calculated in this way are compared with those of the planar base pairs. Optimized geometries were obtained using ab initio molecular orbital theory with electron correlation (MP2/D95**) and density functional theory (B3LYP/D95**). The cooperative contributions are of similar magnitude for each base pair. However, since the A-T overall interaction is weaker, the cooperative interaction provides 31% of its stability versus only 12-16% for G.C. The relatively smaller cooperative contribution to G.C is due to the difficulty of forming three optimal H-bonds between two rigid molecules. Structural modifications that might strengthen one H-bond tend to weaken another. As a result the central H-bond of G.C appears to be compressed by the attractive interaction in the two outer H-bonds. To the extent that these observations can be generalized, they should be important to the design of materials that utilize H-bonding motifs for self-assembly.