Isoguanine (isoG) trimers have been theoretically studied using the density functional theory to reveal the role of H-bonding in the formation of different base aggregations. Similar to the isoG tetrads, the isoG trimer also adopts diverse conformations. Cooperative effects for the H-bonding in the cyclic isoG trimers have been found to be important. As a result of the strong cooperativity, the conformer characterized by the highest symmetry is the most stable among the possible trimers. Vibration mode analysis reveals the influence of the cooperative effects on the H-bond stretching motion. An atoms-in-molecules study of the H-bonds in the isoG trimers suggests that the electronic density topology of the bifurcated H-bond is insensitive to the cooperative effects. The values of the binding energy, the vibration frequency, and the electronic density topology of the noncyclic isoG trimers demonstrate that there is no cooperativity in these open ring structures.