Objective: The aim of this study was to investigate the distribution of HPV genotypes in uterine cervical lesions of Uighur women in the Xinjiang province of China. Methods: A total of 223 formalin-fixed paraffin-embedded cervical tissue specimens from Uighur patients with squamous cell carcinoma (SCC) and cervical intraepithelial neoplasia (CIN) were analyzed with HPV specific general primer pairs MY09/11 by PCR amplification and HPV chip. Results: Among 223 cases, HPV-positive samples accounted for 58.7% (131/223). HPV infection rate increased along with the pathological grade of the specimens, with a clear tendency of normal < CIN 1 < CIN 2 < CIN 3 < SCC. HPV16 infection was the predominate one and reached the highest level in SCC with 96%. HPV18 and 58 were detected only in some specimens as a second infection in addition to HPV16. The infection rate and type of HPV was not closely associated with the histological differentiation of the cervical cancer. Conclusion: HPV16 was the most common type detected in Uighur women with SCC and CIN in the Xinjiang area of China. Together with the high infection rate, this may be the reason for the four-fold higher cervical cancer incidence in this province and in this population, when compared to total China. The prevalence of HPV18 and 58 was relatively low.