Despite strong electrostatic repulsion, like-charged ions in aqueous solution can effectively attract each other via ion-water interactions. In this paper we investigate such an effective interaction of like-charged ions in water by using the 3D-RISM-SCF method (i.e., electronic structure theory combined with three-dimensional integral equation theory for molecular solvents). Free energy profiles are calculated at the CCSD(T) level for a series of molecular ions including guanidinium (Gdm(+)), alkyl-substituted ammonium, and aromatic amine cations. Polarizable continuum model (PCM) and mean-field QM/MM free energy calculations are also performed for comparison. The results show that the stability of like-charged ion pairs in aqueous solution is determined by a very subtle balance between interionic interactions (including dispersion and pi-stacking interactions) and ionic solvation/hydrophobic effects and that the Gdm(+) ion has a rather favorable character for like-charge association among all the cations studied. Furthermore, we investigate the like-charge pairing in Arg-Ala-Arg and Lys-Ala-Lys tripeptides in water and show that the Arg-Arg pair has a contact free-energy minimum of about -6 kcal/mol. This result indicates that arginine pairing observed on protein surfaces and interfaces is stabilized considerably by solvation effects.