OBJECTIVE Study on the frequency and outcome of chlamydia trachomatis (CT) infection of the pregnant women and their babies. METHODS Two hundred and seventy eight pregnant women and their 79 infants were studied with McCoy cell culture, polymerase chain reaction (PCR) and DNA sequence analysis. Isolation of CT was performed in McCoy cell culture, and iodine-stained glycogen-positive inclusions were considered to be positive. CT DNAs were extracted by modified NaI method. Two sets of primers derived from CT common plasmid and major outer membrane protein genes were used in the PCR. Dideoxy-mediated chain-termination method was used for DNA sequence analysis. RESULTS 10.8% (30/278) of the cervical cultures were positive for CT, while the positive rate by PCR was 14.0% (39/278). The vertical transmission rate of CT was 55.0% (11/22). The sequences of DNA amplified from a maternal-infant pair were matched perfectly. The incidence of puerperal endometritis in CT positive women was 28.6%, much higher than 8.1% in those CT negative mothers. Neonatal conjunctivitis and pneumonia in group of CT positive mothers were 45.0% and 30.0%, respectively, much higher than 18.3% and 8.3%, respectively, in that of CT negative mothers (P < 0.05). CONCLUSIONS Perinatal infection caused by CT is very common in China.