The competitive inclusion method was used to determine the stability constants (log K a ) for complexation of natural Ν°-cyclodextrin (1) with aliphatic amino acids in acidic solution. The stability constants (log K a ) for the complexation of modified Ν°-cyclodextrin, mono-[6-(1-pyridinio)-6-deoxy]-Ν°-cyclodextrin (2), with these biological molecules were measured using the differential spectra method. Both natural Ν°-cyclodextrin (1) and chemically modified Ν°-cyclodextrin (2) can recognize not only the size of guest amino acid molecules and the length of their hydrophobic side chains, but also the chirality of enantiotopic L/D-amino acids. The longer the hydrophobic side chain borne on an amino acid, the more stable the complex formed by Ν°-cyclodextrin hosts (1) and (2). Host compounds (1) and ( 2) preferably include L-amino acids, which would benefit from discrimination of L/D-amino acids. Introduction of a positively charged 1-pyridinio moiety to C-6 of Ν°-cyclodextrin apparently enlarges the inclusion ability and enantioselectivity by electrostatic interaction. Comparing the data obtained in acidic medium with those formerly measured in pH 7.20 phosphate buffer solution, a result can be given: when the pH of the medium increases, the complexation ability and selectivity of modified Ν°-cyclodextrin (2) for most amino acids examined here are slightly enhanced, showing the highest enantioselectivity up to 10.3 for L/D-serine.