Squamous cervical carcinoma (SCC) is the most common cancer found in Mexican women. Human papillomavirus (HPV) infection is a prerequisite for this disease. In Mexico little is known about the prevalence of HPV-types and knowledge of the circulating genotypes by region is limited. The aim of this study was to determine the prevalence and genotypes of HPV in biopsies from women with intraepithelial lesions and SCC. A total of 211 cervical biopsies were studied. Histopathological analysis was done and HPV DNA was detected by PCR using MY09/MY11 (MY-PCR) and GP5+/GP6+ (GP+PCR) primers. Viral type was determined by RFLP’s or sequencing. Tissues were classified as low-grade squamous intraepithelial lesion (LSIL) in 123 cases, high-grade squamous intraepithelial lesion (HSL) in 40 and SCC in 48. Prevalence of HPV was 55.3% in LSIL, 65% in HSIL and 91.7% in SCC by MY-PCR. These percentages increased to 83, 77.5 and 100%, respectively, when HPV-negative samples were analyzed by GP+PCR. In 138 of 211 samples (65.4%), HPV was detected by MY-PCR and 43 (20.4%) were positive by GP+PCR. In 166 (91.7%) of 181 infections high risk HPV-types were found. Twelve genotypes were detected (16, 18, 31, 33, 45, 52, 58, 59, 61, 66, 70, 81). Prevalence of HPV 16 in LSIL, HSIL and SCC, were 70.6, 54.8 and 70.8%, respectively and it was the most common type in all cases (67.9%). A significantly higher number of positive samples were detected with MY-PCR and GP+PCR. The high prevalence of HPV infection with high-risk types, especially HPV16, among Mexican women with SIL and SCC, has important implications in the treatment and prophylaxis.