This study aimed to investigate the allele frequencies of CYP2B6 gene in 193 Han Chinese and compared with 91 Uygur Chinese. Five single nucleotide polymorphisms of CYP2B6, 64C > T, 516G > T, 777C > A, 785A > G and 1459C > T, were tested using the polymerase chain reaction-restriction fragment length polymorphism method. The allele frequencies for CYP2B6*2, CYP2B6*3, CYP2B6*4, CYP2B6*5, CYP2B6*6, CYP2B6*7 and CYP2B6*9 in Han and Uygur Chinese were 0.034 and 0.027, 0 and 0.011, 0.091 and 0.033, 0.003 and 0.049, 0.184 and 0.214, 0 and 0.022, and 0.018 and 0.044, respectively, with CYP2B6*4, CYP2B6*5, and CYP2B6*7 being significantly different between these two races (P < 0.05). CYP2B6*6 was the most prevalent allele among all detected variants in Han and Uygur Chinese. The most frequent genotypes were CYP2B6*1/CYP2B6*1 (50.8%), CYP2B6*1/CYP2B6*6 (24.4%), and CYP2B6*1/CYP2B6*4 (7.3%) in Han subjects, whereas the most frequent genotypes in Uygur subjects were CYP2B6*1/CYP2B6*1 (36.3%), CYP2B6*1/CYP2B6*6 (25.3%), CYP2B6*1/CYP2B6*5 (5.5%) and CYP2B6*6/CYP2B6*6 (5.5%). The frequencies of 64C > T mutation in Han and Uygur Chinese were significantly lower than that in American Caucasian (P < 0.05). These results indicate that there were marked ethnic differences in the mutant frequencies of CYP2B6 between Chinese and other ethnic groups. Further studies are warranted to explore the clinical impact of such ethnic differences.