Thirteen pairs of enantiomers belonging to the same structural family (phenylthiohydantoin-amino acids) were analyzed on two polysaccharide chiral stationary phases, namely, tris-(3,5-dimethylphenylcarbamate) of amylose (Chiralpak AD-H) or cellulose (Chiralcel OD-H) in supercritical fluid chromatography with a carbon dioxide/methanol mobile phase (90:10 v/v). Five different temperatures (5, 10, 20, 30, 40°C) were applied to evaluate the thermodynamic behavior of these enantioseparations. On the cellulose stationary phase, the retention, and separation trends were most similar among the set of probe analytes, suggesting that the chiral cavities in this stationary phase have little diversity, or that all analytes accessed the same cavities. Conversely, the retention and separation trends on the amylose phase were much more diverse, and could be related to structural differences among the set of probe analytes (carbon chain length in the amino acid residue, secondary amine in proline, existence of covalent rings, or formation of pseudo-rings via intramolecular hydrogen bonds). The large variability of behaviors on the amylose phase suggests that the chiral-binding sites in this chiral stationary phase have more variety than on the cellulose phase, and that the analytes did access different cavities.