Binding of gold and silver clusters with amino acids (glycine and cysteine) was studied using density functional theory (DFT). Geometries of neutral, anionic, and cationic amino acids with Au3 and Ag3 clusters were optimized using the DFT-B3LYP approach. The mixed basis set used here was denoted by 6-31+G** (union or logical sum)LANL2DZ. This work demonstrated that the interaction of amino acids with gold and silver clusters is governed by two major bonding factors: (a) the anchoring N-Au(Ag), O-Au(Ag), and S-Au(Ag) bonds and (b) the nonconventional N-H...Au(Ag) and O-H...Au(Ag) hydrogen bonds. Among the three forms of amino acids, anionic ones exhibited the most tendency to interact with the Au and Ag clusters. Natural bond orbital analysis was performed to calculate charge transfer, natural population analysis, and Wiberg bond indices of the complexes. Atoms-in-molecules theory was also applied to determine the nature of interactions. It was shown that these bonds are partially electrostatic and partially covalent.