The formation of both isoguanine tetrad and isoguanine pentad alkali metal ion complexes has been reported in experimental studies. We have performed B3LYP hybrid density functional calculations on complexes between alkali metal ions and cyclic isoguanine tetrads and pentads to study a possible preference of specific ions for either pentads or tetrads. All tetrad cation complexes are strongly nonplanar, except for Li+ complexes. Pentads form planar complexes with K+ and Rb+. For all investigated model systems, the polyad alkali ion interaction is the dominant contribution to the interaction energy. In tetrads, the hydrogen bond pattern changes when passing from the tetrad to the metal-ion-containing complexes. In general, the interaction energy between polyads and alkali metal ions decreases with the size of the ion. For Li+, the interaction with the tetrad is stronger, whereas for ions with larger radii the pentad alkali metal ion interaction energy exceeds the corresponding energy for tetrads. A comparison of the interaction energies per base also indicates that the formation of tetrad ion complexes is generally favored for smaller ions, whereas for large ions the difference of the interaction energy per base in tetrads and pentads vanishes. To estimate the performance of the density functional approach for hydrogen-bonded systems, dimers of 6-amino-1H-pyrimidin-2-one, a substructure of isoguanine, have been studied by B3LYP and Moller-Plesset perturbation theory.