BACKGROUND: The incidence of empyema in children in the UK is increasing. The reason for this is unclear. A prospective study was undertaken to investigate the clinical features, aetiology, and outcome of cases of empyema and parapneumonic effusion presenting to a tertiary paediatric respiratory centre between February 1997 and August 2001. METHOD: Routine bacterial culture of blood and pleural fluid was performed for 47 cases. Forty three pleural fluid specimens, culture negative for pneumococcus, were analysed for pneumococccal DNA by real time polymerase chain reaction (PCR). Penicillin susceptibility was determined for DNA positive specimens using complementary PCR assay. Capsular serotype specific antigen detection was by enzyme immunoassay (EIA) using monoclonal antibodies to serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F. Clinical data were obtained from patient notes, supplemented by a postal questionnaire. RESULTS: The median (range) age of the patients was 5.6 (0.6-16.9) years and 70% were male. The median (range) duration of illness before referral to hospital was 5 (0-25) days. Forty five (96%) had received antibiotics before referral; 32 (68%) required decortication and eight (21%) thoracocentesis. Median postoperative stay was 4 days (2-8). Thirty two (75%) pneumococcal culture negative specimens were pneumococcal DNA positive; 17 (53%) of these were serotype 1. All were penicillin sensitive. CONCLUSIONS: Pneumococcus is the major pathogen in childhood empyema and serotype 1 is the prevalent serotype. This has implications for vaccine development and immunisation strategy as the current 7-valent pneumococcal conjugate vaccine does not protect against serotype 1.