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Background: This study was conducted to investigate the distribution of human leukocyte antigen (HLA)-A alleles in advanced squamous cell cervical cancer patients (IIb–IVb SCC) and their relationship to human papillomavirus (HPV) status and clinical outcome. Methods: From May 2012 to March 2016, 231 advanced SCC patients (169 Uyghur and 62 Han individuals) and 197 control subjects (101 Uyghur and 96 Han individuals) from Xinjiang province were genotyped for HLA-A by polymerase chain reaction sequence-based typing (PCR-SBT). The frequencies of HLA-A alleles were compared among the different groups and the correlation of HLA-A frequencies with HPV status and clinical outcome were analyzed. Results: (I) Uyghur patients were more likely to be infected with HPV16 or other types of HPV than Han patients (P=0.001). Han patients responded better to systematic treatment than Uyghur patients (P=0.001); (II) Significantly higher frequencies of HLA-A*01:01, A*03:01 and A*03:02, and lower frequencies of HLA-A*11:01, A*24:02 and A*30:01 were observed in the Uyghur control subjects compared with the Han control subjects (P0.05); (IV) There was no significant association between HLA-A alleles and HPV16 status (P>0.05); (V) FIGO stage and treatment condition were potential independent predictors for disease-specific survival (DSS) (P=0.027 and P=0.004) while only FIGO stage was an independent predictor for DFS (P=0.001). A*30:01 showed a tendency to be an independent protective predictor for DSS (P=0.050; HR=0.132; 95% CI: 0.017–0.996). Conclusions: Women from two ethnic groups displayed varied HLA-A allele distributions. HLA-A*01:01 and A*68:01 alleles increase susceptibility to advanced SCC patients while HLA-A*33:01 serves as a protective allele. HLA-A*30:01 might be an independent predictor for DSS of advanced SCC.