This study aimed to investigate the relationship between HPV and autoimmune disorders. We retrospectively evaluated 62 women who had HPV-DNA positivity in terms of autoimmune disorders (autoimmune antibody positivity, chronic inflammatory diseases and autoimmune diseases). The patients were divided into two groups according to autoimmune disorder positivity (autoimmune positive (n = 30), autoimmune negative (n = 32)) and compared with each other in terms of single and multiple HPV-DNA types, high and low-risk HPV-DNA types, and Pap smear findings. We determined that 48.4% of the HPV-DNA positive patients had autoimmune disorders. We found that 15 of 62 (24.2%) women had more than one type of HPV and HPV type 16 was the dominant type in this study (58.2%). A total of 27.4% of HPV-DNA positive patients had abnormal cytological findings. There was no statistically significant difference between autoimmune groups in terms of the presence of high-risk HPV types, multiple HPV types and abnormal cytological findings (P = 0.531, P = 0.558 and P = 0.234, respectively). The prevalence of autoimmune disorders was high among HPV-DNA positive women. On the other hand, the rate of high-risk HPV type positivity, multiple HPV infections and cytopathological findings were similar between the autoimmune positive and negative groups.