The concentrations of several d-amino acids have been reported to significantly increase in the plasma of patients with chronic kidney disease (CKD). However, the amounts of these d-amino acids are low (around 1% of the l-form or lower), and their analyses were complicated by various interfering compounds in many clinical samples. A highly selective analytical method is thus required to perform the accurate and precise determination of these d-amino acids in the plasma of CKD patients. In the present study, a selective 3D-HPLC system equipped with reversed-phase, anion-exchange, and enantioselective columns has been designed and developed for the determination of the asparagine, serine, alanine and proline enantiomers. For the sensitive analysis, amino acids were precolumn derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole and detected by their fluorescence. The system was validated by using human plasma in addition to the standard amino acids, and results with a sufficient linearity, precision, and accuracy were obtained. The 3D-HPLC system was applied to the plasma of patients with different stages of CKD and all of the target d-amino acids were clearly observed without interferences for all 25 tested patients. Good correlations were shown between the kidney function of the patients and the %d values of the target analytes, especially d-Asn and d-Ser, indicating that the present 3D-HPLC method is useful for the sensitive diagnosis of CKD.