Objective To investigate GJB2 mutation prevalences in the Uigur and Han ethnic groups in Xinjiang, China, and determine the relationship between ethnicity and GJB2 gene mutations. Methods Information regarding ethnicity of patients families was obtained through medical records review and/or patient interview. Blood samples were collected from 61 Uigurs and 66 Hans for direct sequencing of the coding region and intron/exon boundaries of the GBJ2 gene. Results Carrier frequency of GJB2 mutations was similar between the Uigur and Han subjects. The GJB2 35delG mutation was seen only in Uigur patients with hearing loss, whereas the 235delC mutation was identified in both Uigur and Han patients. The allelic Frequency of 35delG mutation was 7.4% (9/122) in Uigur deaf students, but none in Han deaf students (0/128) and Uigur controls (0/196).The allelic frequency of GJB2 235delC mutation in Uigur and Han deaf students was 5.7% and 9.8%, and that of 299-300delAT mutation was 0.8% and 5.5%, respectively. V27I and E114G were the most frequent types of polymorphism. Conclusion We found an Asian-specific GJB2 diversity among Uigurs, and comparable GJB2 contribution to deafness in Uigur and Han patients. The high carrier frequency of 35delG in Uigurs (11.5%) is probably defined by gene drift/founder effect in a particular group. Even though GJB2 mutations have been widely reported in the literature, this discussion represents the first report of GJB2 mutations in Chinese multi-ethnic populations.