The incidence of sexually transmitted diseases among adolescents is increasing worldwide. Genital Chlamydia trachomatis infection is one of the most prevalent sexually transmitted diseases in young women, and undetected disease is highly associated with long-term complications in women. Our goal was to determine the prevalence of cervical Chlamydia trachomatis infection in a sexually active population of female adolescents from Salvador, Brazil, and to describe their socio-demographic, behavioral, and clinical characteristics. 100 sexually active adolescents (10–19 years) were included in this study, between 2008 and 2010. Endocervical samples were obtained during gynecological examination. Inhouse polymerase chain reaction of cervical specimens was used for Chlamydia trachomatis detection. The overall prevalence of cervical Chlamydia trachomatis infection was 31% (95% CI 22–40). There were no statistically significant differences in the age at first sexual intercourse, number of sexual partners, and frequency of condom use between Chlamydia infected and uninfected adolescents. The prevalence of cervical Chlamydia trachomatis infection among adolescents from Salvador was the highest in Brazil up to the present date. These results demonstrate an urgent need for continued and comprehensive prevention strategies along with proper screening for Chlamydia in high-risk populations in order to decrease the rates of infection.