Enantioselective analysis of lactate (LA) in various fermented food/beverage samples including the Japanese traditional amber rice vinegars was performed using a newly designed three-dimensional high-performance liquid chromatographic (3D-HPLC) system. The enantiomers of LA are reported to be possible biomarkers for some diseases such as diabetic mellitus. To evaluate the diagnostic value, the dietary intake should be taken into consideration. Therefore, clarifying the presence of LA enantiomers in our environment is a matter of interest. In the present study, LA enantiomers in a variety of fermented food/beverage samples were determined after the pre-column derivatization with 4-nitro-7-piperazino-2,1,3-benzoxadiazole. Among the fermented products tested, high concentrations of LA enantiomers were observed in a Japanese traditional amber rice vinegar (sample SK, 13.1 and 22.8 μmol/mL for D-LA and L-LA, respectively). The developmental changes of the LA enantiomers during the fermentation/aging processes of the Japanese traditional amber rice vinegar were also studied. The concentrations of D-and L-LA drastically increased in the early stage of the fermentation and attained to the highest concentrations after 1 month, then gradually decreased thereafter. The present results help to illuminate the benefits of Japanese traditional vinegars in the health and food sciences.