Quantum chemical calculations have been carried out to study the structural, electronic, spectroscopic, and thermodynamic properties of five methylmercury-amino acid complexes and their selenium analogues. The structural properties of methylmercury-amino acids are very similar to their Se analogues except for those properties that are directly related to the Se atom which has a larger covalent radius. Characteristic stretching frequencies are observed for Hg−S/Se and Hg−C bonds. Electronic properties of both methylmercury-amino acids and their Se analogues are different from each other, with the S complexes showing stronger electrostatic attractions which leads to stronger bonds to mercury. The methylmercury complexes with selenoamino complexes, however, are thermodynamically more favorable (ΔG of formation from suitable model reactants) than those of the corresponding amino acid complexes. This can be traced to the lower stability of the reactant selenoamino acids. Such different stability and favorability of formation might be responsible for the different physiological activity in biological systems such as the Hg−Se antagonism.