The object of our study was to determine the proportion of atypical respiratory pathogens among patients hospitalized with a community-acquired respiratory infection. From September 1997 to May 1999, 159 patients (57% male, median age 55, range 1-88 y) admitted to 3 regional hospitals for a community acquired respiratory infection, were enrolled in the study. Microbiological diagnosis for the atypical pathogens Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophila was performed with PCR on a throat swab, sputum and/or broncho alveolar lavage (BAL). In addition, Legionella species other than L. pneumophila (L. non-pneumophila species) were detected by PCR. Two serum samples were collected and processed for M. pneumoniae and C. pneumoniae serology. In total, 27 patients (17%) were diagnosed with an atypical pathogen. Infection with M. pneumoniae was detected in 19 patients (12%) (PCR positive n = 7), with C. pneumoniae in 5 patients (3%) (PCR positive n = 0) and with L. pneumophila in 4 patients (2.5%) (PCR positive n = 4). In 54 (34%) patients routine microbiological investigations revealed aetiological agents other than the 3 atypical pathogens, the most frequently diagnosed pathogens being Streptococcus pneumoniae (n = 18), Haemophilus influenzae (n = 17), Gram-negative rods (n = 13), Moraxella catarrhalis (n = 6) and Staphylococcus aureus (n = 6). More than 1 pathogen was found in 13 patients. Atypical pathogens were found more often in the young age group (0-18 y), in contrast to bacterial pathogens that were found more often in the older age groups (> or = 65 y). Atypical pathogens were found less often in patients with a clinical presentation of atypical pneumonia. Legionella species other than L. pneumophila were found by PCR in 13 patients (8%), and in 6 patients in combination with another pathogen. An atypical pathogen (M. pneumoniae, C. pneumoniae or L. pneumophila) was found in 17% of the patients hospitalized with a community acquired respiratory infection, predominantly in the young age group. The role of Legionella non-pneumophila species as pathogen in community acquired respiratory infection needs to be determined. The clinical presentation does not predict the type of pathogen found.