The aim of this study was to evaluate the incidence and morbidities of Chlamydia trachomatis infections in newborn infants. Tissue culture and direct immunofluorescence (DIF) tests were used to detect the presence of nasopharyngeal C. trachomatis infection in 35 preterm and 21 healthy term neonates. All infants were followed up clinically for 3 months, and enzyme-linked immunosorbent assay analysis for serum antichlamydial IgG and IgM was performed on day 15 and week 6. Tissue culture and/or DIF studies showed that 10 of the preterm infants (28.57%), but none of the term infants, were C. trachomatis-positive. The sensitivities of DIF and tissue culture were 40% and 70%, respectively, demonstrating the diagnostic superiority of tissue culture tests for detecting C. trachomatis. Only one asymptomatic preterm infant was found to be positive for antichlamydial antibodies at the 6th week. All C. trachomatis-positive infants were given macrolide antibiotics for 14 days. The study showed that male infants were more frequently infected, but types of delivery, mean gestational ages, mean birth weights, and the need for mechanical ventilation were similar in C. trachomatis-infected and uninfected preterm infants. However, the duration of oxygen treatment was longer in infected preterm infants. Clinical conjunctivitis was more frequent in C. trachomatis-infected infants (60%) than in uninfected infants (24%). C. trachomatis-positive infants had pneumonia more frequently; however, all patients with pneumonia were negative for antichlamydial IgM and IgG antibodies. Macrolide treatment for 2 weeks for nasopharyngeal C. trachomatis positivity may have prevented C. trachomatis related pneumonia, but it may not have significantly influenced the risk of pneumonia caused by other agents. Chlamydial infections may lead to early and late respiratory problems in preterm infants. Nasopharyngeal screening may help physicians detect C. trachomatis infections and provide a means of early diagnosis in this vulnerable patient group.