The comparative structural modeling of cysteine and selenocysteine has provided detailed information about the bond lengths and bond angles. The theoretical and crystallographic data for cysteine are in good agreement with the results obtained using the molecular mechanics technique. Analysis showed that the molecular backbones of cysteine and selenocysteine are close, with the exception of the key bonds C(3)-Se and Se-H, which are significantly increased in comparison with C(3)-S and S-H in cysteine. The calculation of bond lengths and bond angles provided new structural information for selenocysteine. Thus, the differences in thiol and selenol groups are in accordance with the biochemical behavior of the amino acids studied.