The prevalent CYP3A5 *3 and the functional multi-drug resistance gene (MDR1) C3435T show marked interethnic variation among Orientals, Caucasians and Africans. This study aimed to investigate the distribution of CYP3A5*3 and MDR1 C3435T among Chinese ethnic groups. Genotypes of the CYP3A5*3 and MDR1 C3435T were determined in 839 unrelated healthy Chinese subjects by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assays. Frequencies (P of CYP3A5*3 variant alleles observed in Uygur Chinese, Kazakh Chinese and Tibetan Chinese (88.1%, 84.5% and 80.7%, respectively) were Significantly higher than those in Han Chinese, Wa Chinese and Bai Chinese (67.3%, 56.3% and 70.2%, respectively). Significantly higher 3435T variant frequencies (P were observed in Uygur Chinese (58.4%) and Kazakh Chinese (56.8%) compared with Han Chinese (44.2%), Tibetan Chinese (43.9%), Wa Chinese (45.8%) and Bai Chinese (44.2%). These results indicate that there were marked ethnic differences in the mutant frequencies of CYP3A5*3 and MDR1 C3435T among Chinese ethnic groups. Frequencies of those variants observed in Uygur Chinese, Kazakh Chinese, Tibetan Chinese, Wa Chinese and Bai Chinese were intermediate between those seen in Han Chinese and African-American.