Background: Pregnant women with Chlamydia trachomatis and Neisseria gonorrhoeae infections can vertically transmit these microorganisms to their newborns through the birth canal and cause neonatal conjunctivitis secondary to sexually transmitted infections. Objectives: In this cross-sectional study, we aimed to evaluate the prevalence of C. trachomatis and N. gonorrhoeae infections among pregnant women attending a hospital in Tehran, and also determine the vertical transmission rate of these two organisms to the eyes of newborns after vaginal delivery. Methods: Endocervical and conjunctival swabs were collected from pregnant women and their newborns within 24 hours after birth. Demographic and clinical data of participants were obtained using a questionnaire and from the hospital records. Then, DNA was extracted and tested by a multiplex PCR assay to detect C. trachomatis and N. gonorrhoeae in specimens. Results: Genital infections of C. trachomatis and N. gonorrhoeae were detected in 9.6% (11 of 125) and 1.6% (2 of 125) of pregnant women, respectively. Among newborns, ocular infection with C. trachomatis was detected in 2 (1.6%), and no case of N. gonorrhoeae infection was found. Both infected infants were born from asymptomatic infected women. Therefore, the vertical transmission rate of C. trachomatis infection was calculated as 18.1%. Our results also revealed that ocular C. trachomatis infection in neonates is significantly in association with genital C. trachomatis infection in pregnant women (OR = 0.16, 95% CI = 0.03 -0.7, P = 0.002). Conclusions: Pregnant women with asymptomatic infection of C. trachomatis have a key role in the distribution of chlamydial conjunctivitis in newborns. Since ocular prophylaxis in neonates is not effective for chlamydial conjunctivitis, therefore education and screening of pregnant women, as well as treatment of infected cases, remain as the best approach for controlling the disease.