Cervical cancer is the fourth most common type of cancer in women. Worldwide, it is a public health problem with around 604,127 women diagnosed per year and 341,831 deaths. Cervical cancer and persistent high-risk human papillomavirus (HPV) infection are highly associated. However, other factors are also involved, such as viral load, HPV variants, sexual behavior, and genetic factors. The host immune response against HPV has been widely studied and it has shown associations with development of cervical cancer. The human leukocyte antigen (HLA) genes are related to the persistence of HPV infection and progression to cervical cancer because of their role in controlling T-cell mediated immune response to clear the infection. In Ecuador, there is scarce information about HLA and HPV infection with high-risk genotypes in the population. This study aimed to identify host-specific HLA alleles in women with cervical intraepithelial neoplasia (CIN) II and III, and cancer infected with HPV-16, 58, and 52. In this study, we included 51 samples previously identified as positive for HPV-16, 58, and 52 from 12 Ecuadorian provinces. As a result, we found that HLA-A*02, HLA-B*35, HLA-C*04, HLA-DRB1*04, and HLA-DQB1*03 alleles were the most frequent, these alleles have been associated with cervical cancer in previous studies; nevertheless, we did not find a statistically significant association between HLA alleles, HPV genotype, and histopathological lesion. This is a baseline study to uncover possible relationships between HLA and HPV to elucidate why this virus can develop a persistent infection in some women leading to the development of cervical cancer.