Background:Chlamydia trachomatis (C. trachomatis) is the most common sexually transmitted bacterial infectious disease in the world. Moreover, it plays a role in spontaneous abortion. The accuracy of PCR in detection of C. trachomatis infections has been shown in several studies. Objectives: The frequency of spontaneous abortion and known side effects and statistics vary in Chlamydia trachomatis infection in women with spontaneous abortion and different ways to identify and determine the prevalence of Chlamydia trachomatis are used. Materials and Methods: Four sterile Dacron swabs were used to collect specimens from endocervix and vagina from women with miscarriage. DNA was extracted by AccuPrep Genomic DNA extraction kit. The nested PCR procedure was performed with two pair primers. This study was conducted on women referred to Medical Centers of Tehran, Iran in 1391. Results: The number of intercourses per week and history of miscarriage can be known as the risk factors of abortion. Frequency of C. trachomatis in endocervix was 13.25%; the amount of vaginal infection among this group was 19%. Conclusions: Nested PCR as a sensitive Chlamydia trachomatis detection test and endocervical specimens has been offered to detect this bacterium in spontaneous abortion. Besides, C. trachomatis screening among pregnant women can be suggested to prevent abortion.