Children (n = 117; mean age 2.4 +/- 2.9 years) were diagnosed as having community-acquired pneumonia (CAP) using clinical symptoms, chest X-rays, and hematological data. The causative pathogen was determined using real-time polymerase chain reaction (PCR) (6 bacteria), multiple reverse transcription-PCR (MPCR; 11 viruses), bacterial culture, and serology. The initial chemotherapy was evaluated based on the pathogens identified using PCR. We found 27 viral cases (23.1%), 25 bacterial cases (21.4%), 45 mixed infections with virus and bacteria (38.5%), 10 Mycoplasma pneumoniae (8.5%), 7 mixed infections with M. pneumoniae and another pathogen (6.0%), 1 Chlamydophila pneumoniae (0.9%), and 2 unknown pathogens (1.7%). Streptococcus pneumoniae and Haemophilus influenzae accounted for 58 (49.5%) and 27 (23.0%) of the cases, respectively. The median values (50%) of the white blood cell count (WBC) and C-reactive protein (CRP) using the box-and-whisker and plot method, respectively, were 11.7 x 10(3) mm(-3) and 1.4 mg/dl in viral infections, 15.6 x 10(3) mm(-3) and 4.8 mg/dl in mixed infections with virus and bacteria, 17.8 x 10(3) mm(-3) and 6.3 mg/dl in bacterial infections, 6.7 x 10(3) mm(-3) and 1.4 mg/dl in M. pneumoniae infections, and 21.5 x 10(3) mm(-3) and 6.4 mg/dl in mixed infections with M. pneumoniae and other bacterial infections. Sulbactam/ampicillin (n = 61), carbapenems (n = 12), and ceftriaxone (n = 7) were selected for the patients suspected of having bacterial infections alone or mixed infections with bacterial and viruses in accordance with our criteria defined tentatively. For those with M. pneumoniae and C. pneumoniae infections, azithromycin or minocycline was initially used. Treatments averaged 3-5 days. The empirical chemotherapy was improper in 9.4% of cases in relation to the etiologic agents finally identified. We conclude that rapid and comprehensive identification using PCR can provide optimal antimicrobial chemotherapy for CAP patients.