Background: Endocervical infection by Chlamydia trachomatis is considered one of the leading causes of infertility worldwide. During pregnancy, it can lead to serious complications such as premature rupture of membranes and premature births. Aim: To determine the prevalence of genital infection by C. trachomatis in pregnancy and infertile women from Mexico City. Methods: The detection of C. trachomatis was performed by real-time PCR with the commercial kit COBAS (R) TaqMan CT Test v2.0 (Roche Molecular System). Results: We analyzed 2,352 endocervical swabs; 102 were positive (4.3%). Age prevalence showed that pregnant adolescents (15 to 19 years of age) had the highest risk of infection (10.9%, RR = 3.23 [95% IC: 1.79-5.84]), followed by young women aged 20 to 24 years, with a prevalence of 5.6% (RR =1.65 [95% IC: 0.82-3.34]). Discussion: The results indicate that the prevalence is within the range reported worldwide. However, pregnant adolescents were those with a higher prevalence than infertile women were. Conclusion: A systematic screening of C. trachomatis infection in women younger than 24 years of age, and in pregnant women is necessary to reduce the incidence of infertility and perinatal complications.