The existence of D-amino acids in mammals has been increasingly reported, and clarified that D and L enantiomers have different biological functions, distributions and metabolic pathways. Some D-amino acids were also reported to have a correlation with diseases, and the screening of biomarkers based on quantitative enantioselective metabolomics is highly expected. However, the amounts of most D-amino acids, especially the metabolic-related chiral amino acids, are usually at trace levels in biological samples. Therefore, highly selective and sensitive analytical methods are essential for their accurate determination. In this focusing review, multi-dimensional high-performance liquid chromatographic (HPLC) systems for the precise determination of metabolic-related chiral amino acids are introduced with their application to biological samples. For the highly-sensitive determination, target amino acids were precolumn-derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F). The multi-dimensional HPLC systems were composed of a reversed-phase column in the 1 st dimension and an enantioselective column in the 2 nd dimension. By using these systems, various proteinogenic amino acids were clearly observed in the tissues and physiological fluids of rodents. The existence of metabolic-related chiral amino acids in various biological samples were also elucidated.