A two-dimensional chiral high-performance liquid chromatographic (2D-HPLC) system has been established for the analysis of extraterrestrial amino acids. As the targets, 8 chiral amino acids (alanine (Ala), valine (Val), 2-aminobutyric acid (2AB), norvaline (nVal), N-methylalanine (N-MeAla), isovaline (iVal), 3AB and 3-aminoisobutyric acid (3AIB)) and 5 non-chiral amino acids (glycine (Gly), β-Ala, γ-aminobutyric acid (GABA), sarcosine (Sar) and 2AIB) were selected. These amino acids were tagged with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), and non-enantioselectively separated by a capillary monolithic ODS column in the first dimension. The target fractions were automatically introduced into the second dimension and further separated by Pirkle-type enantioselective columns. By using this system, the 2D-HPLC separation of 21 components in small particles of a carbonaceous chondrite (Yamato 791191, Antarctic CM2 meteorite) could be successfully performed, and all of the target amino acids were observed. The D/L ratios of the chiral molecules are almost 50/50 for all of the tested proteinogenic and non-proteinogenic amino acids.