There are few studies on the circulation of Human Papilloma Virus (HPV) in indigenous Ecuadorian women. The aim of the study is to determine the circulation of HPV and identify cytological alterations in cervical samples of indigenous Ecuadorian women and to define the behavior of some socio-demographic and clinical-epidemiological variables. An analytical cross-sectional study was done between July 2017 and September 2018 to determine the presence of cytological alterations and HPV infection in 100 indigenous women between 15 and 55 years of age, residing in Cañar, Ecuador. The association between socio-demographic and clinical-epidemiological variables with viral infection was investigated. Was obtained a 98% of negative cytology for malignancy and 2% of cervical lesions. Cases with high-grade lesions were not diagnosed. In general, a 34% (34/100) tested was positive for HPV, predominating oncogenic genotypes. HPV 31 was the most frequent in 41.2% (14/34) of cases followed by HPV 16 in 20.6% (7/34). Women between 20 and 30 years of age were five times more likely to be infected with HPV (44.1%, 15/34). The frequency of infection was significantly higher in single women and in those who reported having 2 to 3 births. Infection with HPV 16 was associated with the use of hormonal contraceptives, in 57.1% (4/7) of the cases; p = 0.005, RP = 12.44 IC95% (2.40-64.62). The high prevalence of oncogenic HPV infection indicates the need to incorporate this indigenous population into early detection programs for cervical cancer.