Objective To explore the role of acute infection of Chlamydia pneumoniae (Cpn) in respiratory diseases. Methods Microimmunofluorescence test was used to detect IgG antibodies for Cpn in serum obtained from 93 inpatients and PCR was used to test Cpn in detection of Cpn DNA in throat specimens from 55 of the 99 patients. Results Acute Cpn infection was diagnosed in 35.5% of the respiratory diseases. Antibodies for Cpn (titer of ≥512) were present in 47.6% of the pneumonia group, which may suggest that during 1998 to 1999, Cpn caused an epidemic in Beijing. They were also present in 50% of asthma group, 50.0% of pulmonary heart disease group and 26.3% of lung cancer group. Only five patients (9.1%) were positive by PCR. There exists discrepancy between serological and PCR results. Conclusion Detection of IgG antibodies for Cpn conduces to diagnosis of acute Cpn infection and give advice for appropriate therapy.