We used a new polymerase chain reaction (PCR) system to identify the 16S rRNA gene of Mycoplasma pneumoniae and to diagnose lower respiratory tract infections caused by the microorganism. Nasopharyngeal swabs collected from 21 patients (22 episodes) tested positive for M. pneumoniae with the PCR. The age distribution of the patients was between 2 and 13 years. The diagnosis, including concomitant infection, was as follows: pneumonia (n = 11), acute bronchitis (n = 10), bronchial asthma (n = 4), and acute otitis media (n = 1). Six patients had bacterial superinfections. Positive findings for M. pneumoniae were noted together with exacerbation of asthma symptoms, suggesting that M. pneumoniae infection may play the role of an inducer. The PCR system constructed by us will contribute to revealing the clinical features of M. pneumoniae infection, and as a result, an appropriate chemotherapeutic agent can be chosen. We propose the usefulness of this PCR system to detect the microorganism in younger children.