Chiral amino acid analysis, especially the determination of trace levels of D-enantiomers, is currently gathering attention in a variety of research areas including the food/clinical sciences. These D-amino acids had long been believed to be absent in the higher animals. However, by the advances of analytical technologies, some of the D-enantiomers are found in mammals including humans and increasingly recognized as novel physiologically-active substances and/or biomarkers. For the determination of these D-amino acids and related compounds in real world samples, utilization of sensitive and selective methods is essential and multi-dimensional HPLC is one of the straightforward approaches. In the present review, two/three-dimensional HPLC methods and biological/medical applications focusing on our current studies are summarized.