Chlamydia trachomatis is the most common bacterial pathogen causing sexually transmitted infections in Dutch adults. As prenatal screening for C. trachomatis and treatment of pregnant women is not routine practice in the Netherlands, perinatal transmission of C. trachomatis may therefore occur. We evaluated the presence of C. trachomatis in infants less than six months of age who presented with respiratory complaints to the Erasmus MC-Sophia hospital. Respiratory specimens, primarily nasopharyngeal swabs, were tested for C. trachomatis, respiratory viruses and Mycoplasma pneumoniae using PCR, viral isolation in cell cultures and direct immunofluorescence. C. trachomatis respiratory tract infection was confirmed to be relatively common with detection in 10 of 148 (7%) infants tested. C. trachomatis had not been tested for by the attending physicians, but was the second most frequently detected respiratory pathogen after human Respiratory Syncitial Virus, which was found in 41 (28%) infants.