Background: Genotype distribution and prevalence of human papillomavirus (HPV) among women vary from different regions and crowds, prophylactic HPV vaccin could prevent some diseases related to HPV, which include cervical precancerous lesions and cancer. Baseline surveys prior to mass HPV vaccination are critical to determine vaccine efficacy and detect changes in HPV type after vaccination. Objective: The aim of this study is to study the HPV type-specific prevalence in 698 women with cytological abnormalities, aging from 18 to 77 years old. Additionally, the association between HPV infection and cervical disease was investigated as well. Methods: A total of 698 cervical specimens of cytological abnormalities were collected from the First Affiliated Hospital of Xinjiang Medical University. The Thinprep liquid-based cytologic test (TCT) was performed and the cytological status was classified according to Bethesda 2001. The samples were tested HPV genotype by the PCR-based hybridization gene chip assay. Results: Overall, the HPV prevalence was 54.87%, and it was shown to be age dependent, and with the decreasing and zigzag prevalence until the age of 55 years. 204 patients (53.26%) were infected with pure high-risk HPV, 139 (36.30%) with pure low-risk HPV, and 40 (10.44%) with mixed HPV types. HPV16 was the most common type (35.36%), followed by HPV58 (13.62%) and HPV52 (9.15%). In this study, 386 (55.30%) were affected by ASCUS, 11 (1.58%) by ASC-H, 137 (19.63%) by L-SIL and 151 (21.63%) by H-SIL. Women with a cytology result of ASCUS, ASC-H, L-SIL and H-SIL had the infection of HPV 39.12%, 54.17%, 70.80% and 80.79% respectively. Conclusions: In conclusion, this study presents the first investigation about the prevalence of HPV infection and HPV genotype distribution in Xinjiang women who have abnormal cytological tests. Prior to HPV immunization in Xinjiang's population, our results could be baseline data and validation set, which provide robust available estimates of the prevalence of type-specific HPV.