This study investigates the complexes formed between amino acids, which are the natural degradation products of organic matter, and smectites. Thus, the adsorption and desorption behavior of cysteine and Na-, Ca-, Cu-homoionic smectites with different layer-charge location, a montmorillonite, and a beidellite, were studied. The clay samples were treated with Na, Ca, and Cu 1 N solutions and then with a 0.2 M cysteine solution. To test smectite-cysteine stability at acidic pH, the solids obtained were repeatedly treated with distilled water acidified to pH = 5. All treated samples were characterized by thermal, X-ray diffraction, chemical, and infrared analyses. The results showed that: 1) Na- and Ca- rich smectites adsorbed and retained small amounts of cysteine, and did not show interlayer cation-cysteine complexes, whereas the amino acid was strongly retained in the interlayer by Cu-rich smectites; 2) d(001)-values for Na- and Ca-rich smectites showed little or no expansion, whereas for the Cu-rich smectites the intercalation of the organic molecule produced a swelling of the structure; 3) the interaction mechanism of homoionic smectites with cysteine in an aqueous medium occurs by weak interactions, (e.g., van der Waals interactions, hydrogen bonding, dipole-dipole interactions, and other electrostatic forces such as entropy-driven hydrophobic bonding), and/or by complexes involving interlayer cations and organic ligands. The formation of a stable chelate complex with the saturating ion permits cysteine to be adsorbed by Cu(II)-rich smectites and to be resistant to migration in soils and groundwaters.