A fully-automated two-dimensional (2D) HPLC system for the determination of serine (Ser), threonine (Thr) and allo-threonine (aThr) enantiomers was developed. The system was validated and applied to the determination of the target hydroxy amino acid enantiomers in vinegar samples including the Japanese traditional amber rice vinegar. The Japanese traditional amber rice vinegar is one of the typical natural fermented products containing high levels of D-amino acids, and the clarification of the amounts of hydroxy amino acid enantiomers is expected. For the on-line 2D-HPLC system, a narrowbore ODS column (Singularity RP18, 1.0 x 250 mm) was used in the first dimension, and an originally-designed Pirkle-type chiral stationary phase (Singularity CSP-013S, 1.5 x 250 mm) was utilized in the second dimension. The target hydroxy amino acids were derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F) and detected by their fluorescence (ex. 470 nm, em. 530 nm). The concentrations and the %D values were compared among a grain vinegar, a widely-distributed black vinegar and Japanese traditional amber rice vinegars (fermented/aged 1 or 5 years by microorganisms in an earthenware jar). The amounts of hydroxy amino acid enantiomers were low (0.21-0.38 μmol/mL, only L-forms) in the grain vinegar, and relatively high amounts of the L-forms were observed (1.05-1.61 μmol/mL) in the widely-distributed black vinegar. On the other hand, clear peaks of the D-forms (0.16-0.86 μmol/mL for D-Ser, 0.02-0.11 μmol/mL for D-aThr) as well as high amounts of the L-forms (2.27-2.51 μmol/mL for L-Ser, 1.85-2.10 μmol/mL for L-Thr) were observed in the Japanese traditional amber rice vinegars. The amounts of D-Ser and D-aThr clearly increased with increasing the fermentation/aging period. This is the first report showing the profiles of the hydroxy amino acid enantiomers simultaneously, and further investigations using various fermented food/beverage samples are expected.