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BACKGROUND Chlamydia Trachomatis is an obligate intracellular bacteria characterized by a biphasic development cycle of replication. The organism is recognised as one of the major causes of sexually transmitted diseases (STD) in the world. However, most health care facilities in Nigeria do not routinely screen for Chlamydia antigen in gynaecological and other clinic, hence the need for this study. OBJECTIVE To determine the prevalence and factors associated with genital chlamydial Trachomatis infections among women attending infertility and family planning clinics in Federal Medical Centre, Abeokuta. METHODS A case controlled study of the prevalence of chlamydial Trachomatis infection in 183 women of the infertility clinic (study group) and 183 women of the family planning clinic (control group) attending the Federal Medical Centre, Abeokuta. Endocervical swabs were obtained for Chlamydia rapid test and the results were compared with the HSG of the infertile women.