It has been suggested that cation-pi interactions constitute a strong, specific driving force that plays a key role in molecular recognition. The importance of such interactions in biological systems is explored here via two complementary approaches. The first one relies on an analysis of the association of phenylalanine, tyrosine, and tryptophan with arginine and lysine in 1718 representative protein structures, highlighting orientational preferences in cation-pi complexes. The second one consists of an MP2/6-311++G**//MP2/6-31G** ab initio investigation of the dimers formed by relevant models of the amino acid side chains that are engaged in cation-pi interactions. The estimated induction contribution to the binding energies confirms that polarization effects are significant. The ability of commercial, two-body potential energy functions to describe cation-pi interactions accurately is also investigated, and the inclusion of correcting parameters in the force field is discussed. Put together, these results provide new insights into the nature of cation-x association in proteins.