The objective of this study was to estimate the prevalence of Human papillomavirus (HPV) genotypes and Chlamydia trachomatis (CT) infections among adolescents and young adult women and to identify the risk factors associated. This study included 276 sexually active participants, classified as adolescents (15-19 years) and young adult women (20-24 years) that realized conventional cytology and were tested for 27 HPV genotypes and for CT. Bivariate and multivariate analyses were performed to evaluate the factors associated with both infections. The prevalence of HPV infection was 50.7% in adolescents and 43.0% in young adult women. The HPV-16 was the most prevalent (27.7%), followed by HPV-68 (6.9%), HPV-52 (6.2%), HPV-39 (4.6%), and HPV-73 (4.6%). The prevalence of CT infection was 11.5% among adolescents and 6.2% among young adult women. Cytological abnormalities were found in 14.2% among adolescents, of which 80.9% were positive for HPV and 10% of young adult women of which 84.6% were positive for HPV infection. HPV16 and HPV 68 were detected in 35.7% and 32.1% of cases with cytological abnormalities. Factors independently associated with HPV infection obtained by multivariate analysis were unmarried or divorced marital status and the presence of cytological abnormalities. The same variables were analyzed for the association with CT infection, and the association with cytological abnormalities remained significant. HPV and CT infections are very prevalent in adolescent and young adult women; these findings reinforce the need of early vaccination, prior to the onset of sexual activity, and justify implementation of molecular screening tests.