Background: Chlamydia trachomatis is one of the most common sexually transmitted disease agents. Cervical intraepithelial neoplasia (CIN) has been independently associated with serological evidence of chlamydial infection. This study therefore was aimed to determine the prevalence of C. trachomatis and the association between Chlamydia trachomatis infection and cervical intra-epithelial lesion.Methods: It is a cross-sectional case control study carried out at the Lagos University Teaching Hospital (LUTH) with the study participants selected into 2 groups: the case group (women with abnormal smears) and the control group (women with normal Pap smear). Relevant information was obtained using a structured interviewer-administered questionnaire. Endocervical swab sample was collected and analysed by Polymerase Chain Reaction (PCR) test. Data analysis was done using Epi-Info statistical package (version 3.4.3).Results: The overall prevalence of C. trachomatis was 27.7% with a decreasing trend noted with age (P <0.05). The majority of women with C. trachomatis were in the reproductive age group of 25-45 years. 50% of women with abnormal smears were positive for C. trachomatis, compared to only 16.7% of the controls (X2 = 10.95; P = 0.001). There was no statistically significant association between prevalence of C. trachomatis and cervical cytological types (X2 = 1.892; P = 0.595)Conclusions: The study revealed an association between Chlamydia trachomatis and precancerous lesions of the cervix. Routine screening and treatment of sexually active adolescents and women in the reproductive age group is recommended as an indirect measure to reducing the incidence of cervical cancer in Nigeria
