Background Some important factors for the most common sexually transmitted infection (STI) in the world caused by human papillomavirus (HPV) are well defined as early sexual activity, use of contraceptives, tobacco smoking, immunological and genetic factors. This study aimed to investigate the relationship between polymorphisms, GSTM1 and GSTT1, and HPV infection and associated risk factors in a group of women assisted in the public health system in southwestern Paraná, Brazil. Methods and results A case-control study was designed, in which the case group consisted of 21 women with HPV, matched by age, with the control group, 84 women without the virus. Viral detection was conducted via Polymerase Chain Reaction (PCR) and GSTM1 and GSTT1 genotyping by Multiplex PCR. The results showed that the GSTT1 null allele was a protective factor against infection (ORadj: 0.219; 95% CI 0.078-0.618; p=0.004). No relationship was observed for the GSTM1 gene. The smoking habit was defined as a risk factor (ORadj: 3.678; 95% CI 1.111-12.171; p=0.033), increasing the chance for the presence of HPV by up to 3.6 times.Conclusion In short, this study showed in an unprecedented way, the relationship between GSTM1 and GSTT1 genetic polymorphisms and HPV. The relationship found portrays protection from viral infection and not from susceptibility in the female population of southern Brazil.