Introduction: Chlamydia trachomatis is a common and curable STI which can be symptomatic or asymptomatic. Nowadays, PCR is a very sensitive diagnostic tool for detecting Chlamydia in urine and can be used in routine screening procedures as a noninvasive test. There are few studies on the prevalence of C. trachomatis in Iranian women and most of them have small sample sizes which are not suitable for epidemiological deductions. The aim of this study was to estimate the prevalence of urogenital C. trachomatis infections by PCR on urine samples of women in their fertility years and to evaluate the necessity of screening for asymptomatic infections in Iranian women.Materials & Methods: This WHO supported descriptive-analytical and cross-sectional study was performed on 1052, 15-49 year-old women. Participants were selected randomly from attendees of 5 Obstetric-Gynecologic clinics in Tehran during summer and fall of 2003. The research material consisted of a questionnaire and urine samples which were transported to Avesina Research Institute daily to extract their DNA and prepare them for PCR tests. The gathered data were analyzed by SPSS, version 11, and evaluated statistically by t-test, Chisquare, variance analysis and logistic regression, while considering p<0.05 as significant.Results: The mean age of participants was 28.52±6.36 years. 56.2% of them had high school education, 94.2% were married, 91.8% were housewives, 32.5% were pregnant, 93.8% were sexually active, 99% of them were monogamous and 48.1% were on contraceptive methods. Among sexually active and non-pregnant participants, 10.4% were taking OCPs, 8.7% were using condoms, 16.3% had IUDs and the rest were on other contraceptive methods. In their reproductive history, 39% had vaginal discharges, 12.9% pelvic pains, 1% ectopic pregnancies, 21.2% abortions, 6.5% premature deliveries, 2.7% low birth weight infants and 7.2% were infertile. 129 subjects, (12.3%), had positive PCR tests. Statistically, there was no significant relationship between subjects, reproductive and personal histories of the subjects with the test results.Conclusion: Based on the estimated prevalence, it seems that chlamydial infection is prevalent in the studied population. In populations with prevalence higher than 4%, screening programs are recommended, so that Chlamydia screening can be considered as a part of health care programs in Iran to reduce the burden of the disease.