AIM: To study the genetic polymor-phisms of CYP2C9 and CYP2C19 by using 3-dimense polyacrylamide gel-based microarray method in healthy male Chinese subjects, providing original technology and research method for clinical rational administra-tion. METHODS: 207 healthy male Chinese volun-teers were recruited and their genomic DNA were iso-lated. The genomic fragments containing CYP2C9~* 3,~*13 and CYP2C19~*2,~*3 polymorphic sites were amplified respectively to prepare 3-dimense polyacryl-amide gel-based micmarrays. After hybridized by fluo-rescent labeling probes, the micmarrays were scanned to obtain genotyping results of CYP2C9 and CYP2C19. The analytic results were confirmed by direct sequenc-ing. RESULTS: In 207 volunteers, the number of subjects with CYP2C9~*1/~*3, CYP2C9~*1/~*13 and CYP2C9~*3/~*3 genotype were 11, 1, and 1, respec-tively. The frequencies of CYP2C9~*3 and CYP2C9~* 13 alleles were 2.90% and0.24%, respectively. The incidence of CYP2C9 poor metabolizers was 0.48%. With regard to CYP2C19, heterozygous variants were 97 and homozygous variants were 26. The frequencies of CYP2C19~*2 and CYP2C19~*3 alleles were 32.85% and 3.62%, respectively. The incidence of CYP2C19 poor metabolizers was 12.56%. The distribution of the four alleles were all coincident with Hardy-Weinberg law. CONCLUSION: 3-dimense polyacrylamide gel-based microarray method could serve as an advanced platform for clinical genotyping. The polymorphisms of CYP2C9 and CYP2C19 are frequent in Chinese popula-tion. Detecting the Genotyping CYP2C9 and CYP2C19 gene before administration could optimize related clini-cal drugs therapy, with the purpose of high efficiency and low incidence of adverse reactions.