Thiol-containing amino acids have been known to act as chelating ligands with three potential coordination sites: thiol, amine, and carboxyl groups. Since early reports on the iron-catalyzed oxidation of cysteine in 1884 and the copper-chelating therapy of d-penicillamine in 1956, more than 200 coordination compounds with thiol-containing amino acids have been developed and structurally characterized. The co-presence of hard (amine and carboxylate) and soft (thiolate) Lewis bases in the ligands enables them to bind to most metallic elements ranging from Group 3 to Group 15 in various coordination modes. In addition, the presence of a thiolate group leads to the formation of multinuclear structural motifs with sulfur bridges in this family of coordination compounds. Notably, the recent development of a metalloligand approach using isolated metal complexes with thiol-containing amino acids, which contain available coordination sites for secondary metal ions, has contributed to the rational creation of a variety of multinuclear and metallosupramolecular coordination compounds. This review provides an overview of the synthesis, structures, and properties of coordination compounds derived from thiol-containing amino acids, focusing on cysteine and penicillamine as multifunctional ligands.