One of the challenges in planning the treatment of respiratory tract infection in children is identifying the causative agent. The objective of the present study was to investigate the incidence of Mycoplasma and Chlamydia in the etiology of respiratory tract infections of children. The present study included 100 children, three months to 12 years of age, admitted to the outpatient department of pediatrics with such respiratory symptoms as fever, cough and respiratory distress. Following a detailed clinical history and physical examination, complete blood count, erythrocyte sedimentation rate, peripheral blood smear and chest X-ray were obtained from each patient. At admission, IgG and IgM for Mycoplasma pneumoniae, Chlamydia pneumoniae, Chlamydia trachomatis and Chlamydia psittaci were determined serologically. Positive antibody titer was found for Chlamydia and Mycoplasma in 18 (18%) of the patients. It was found that 2% of the patients had acute C. pneumoniae infection. When the subjects who had infections in the past or had re-infection were also considered; 6% were infected with C. pneumoniae, 3% with C. trachomatis, 1% with C. psittaci and 8% with M. pneumoniae. The presence of eosinophilia (≥ 4%) or the presence of siblings in the house were considered as factors favoring Chlamydial infections. High antibody titers for M. pneumoniae and C. pneumoniae were found more frequently after the age of two. Patients older than two years should be evaluated carefully for antibiotic treatments against atypical agents in pediatric lower respiratory tract infections.