HLA-DQA1 and -DQB1 genes were investigated in two Chinese minor natinalities, Uygur and Kazak using PCR-RFLP genotyping method. Of the 8 DQA1 alleles, DQA1 *0301 was the most common in Uygurs and Kazaks. DQA1 *0401 and *0601 were the rarest alleles in Uygurs and *0601 in Kazaks. Of the 16 DQB1 alleles tested, DQB1 *0201 and *0301 were the most frequent alleles in Uygurs and Kazaks. DQB1 *0502, *05032 and *0504 in Uygurs, *05032, *0504 and *0605 in Kazaks were absent. Neither DQA1 nor DQB1 difference was found between the two populations. From the phylogenetic tree based on the gene frequencies of HLA-DQA1 and -DQB1 in Uygur, Kazak and other 25 related ethnic groups, we suggest that Uygurs and Kazaks have a closer relationship, and they are closer to Mongoloid, not Caucasoid.