Genital chlamydial infection in women is not routinely diagnosed in most hospitals within developing countries despite its public health significance. This is probably as a result of lack of skills and the high cost of technology necessary for the diagnosis. These, and the fact that about 80% of women infected with the organism may not experience any significant symptom, pose the biggest challenge to the diagnosis and control of chlamydial genital infection. Men, women and infants may be affected but women bear an inordinate burden because of their increased risk for adverse reproductive consequences. This cross-sectional study was carried out between February and July 2013, to determine the prevalence of genital Chlamydia trachomatis infection in 365 women of reproductive age group attending the GOPC, ABUTH, Shika-Zaria. Endocervical swabs samples were collected from the enrolled subjects and analyzed using a glycogen assay kit and PCR. A structured questionnaire was also administered to obtain pertinent data. Of the 365 patients studied, genital Chlamydia trachomatis was found to be prevalent in 26%. Statistical significant factors associated with infection included low educational status, early age at sexual debut and marriage (≤ 2 17years), multiple sex partners and lack of use of condoms during sexual intercourse. Sensitivity and specificity of the glycogen assay (using the PCR as standard) was 86.8% and 40% respectively. The prevalence obtained in this study was high; there is therefore, the need for increased awareness in the community about genital chlamydial infections, provision of effective screening programmes and multiple diagnostic centers for prevention, early detection and treatment of Chlamydia trachomatis infection, thereby reducing the morbidity and subsequent complications associated with C. trachomatis infection especially in women