The catalytic site of selenium-dependent glutathione peroxidase (GPx) comprises three amino acid residues, i.e. selenocysteine (Sec), tryptophan (Trp) and glutamine (Gln). Although the importance of this catalytic triad in the enzymatic antioxidative function is well evidenced, the interaction modes among the three amino acid residues, as well as the mechanistic roles of the Trp and Gln are not yet well elucidated. Meanwhile, the presence of a catalytic tetrad, which includes an additional proximate asparagine (Asn) residue, has also been proposed at the GPx active site. There are two possible modes of the interactions between the Sec and the other amino acid residues, i.e. NH⋯Se hydrogen bond and non-bonded O⋯Se interaction, both of which would be used by GPx depending on its oxidation state. A wide range of organoselenium compounds, i.e. ebselen and its analogues, aromatic selenium compounds with functional groups, selenocysteine and the related water-soluble compounds, and designed Sec-containing peptides, have been investigated to date as mimics of GPx. We overview cumulative research results on the molecular mechanism of the antioxidative function of GPx and the design of GPx mimics from the viewpoint of weak interactions that would exist between the selenium active center and the nearby heteroatom-containing functional groups at the GPx active site.