BACKGROUND:There are few genetic data related to nonsyndromic cleft lip and palate in Xinjiang Uygur population. OBJECTIVE:To investigate the relationship between interferon regulatory factor 6 (IRF6) and non-syndromic cleft lip and palate in Xinjiang Uygur population. METHODS:A total of 100 Uyghur patients with non-syndromic cleft lip and palate from Xinjiang were included as case group, and meanwhile, 60 children with upper respiratory infection were enrol ed as controls. Next-generation sequencing was used to detect coding region, 5’UTR and 500 bp before exon1 of IRF6 gene, and sequencing results were compared with the information on the genome database. RESULTS AND CONCLUSION:Eleven high-frequency SNPs were found:rs861019, rs7552506, rs2235377, rs2235371, rs2013162, rs7545538, rs7545542, rs12403006, rs846808, rs34743335, rs2235373. The frequencies of al eles of loci rs7545538 (C>G, P=0.007), rs7545542 (C>T, P=0.044) and rs2235373 (G>A, P=0.049) were significantly different in the case group and control group;the genotype distribution of rs7545538 showed significant difference between the case group and control group (P=0.037);the genotype distribution and the frequency of al eles of other loci had no significant difference between the case group and control group (P>0.05). Two blocks were identified in the 11 high-frequency SNPs. There were four common haploid types in Block 1:CCGGT>CCGAT>CACAT>TAGAC, and the most significant single type was CCGAT (P=0.032). There were three common haploid types in Block 2:TAC>ATG>TAG, and the most significant single types were TAC (P=0.009) and TAG (P=0.003). These findings indicate that IRF6 gene polymorphisms are probably associated with the occurrence of non-syndromic cleft lip and palate in Xinjiang Uygur population.