BACKGROUND The indication for chest physical therapy as an adjunct to the treatment of children hospitalised with acute pneumonia remains controversial and there is a lack of robust scientific evidence for the effectiveness of this modality in these patients. METHODS A randomised controlled trial was conducted in two tertiary hospitals in southern Brazil. Children aged 29 days to 12 years hospitalised with pneumonia between February and October 2006 were recruited; 51 were randomly allocated to the intervention group (chest physical therapy plus standard treatment for pneumonia) and 47 to the control group (standard treatment for pneumonia alone). The primary outcome was time to clinical resolution. The secondary outcomes were length of stay in hospital and duration of respiratory symptoms and signs. RESULTS There were no significant differences in terms of median time to clinical resolution (4.0 vs 4.0 days, p = 0.84) and median length of hospital stay (6.0 vs 6.0 days, p = 0.76) between the intervention and control groups. The intervention group had a longer median duration of coughing (5.0 vs 4.0 days, p = 0.04) and of rhonchi on lung auscultation (2.0 vs 0.5 days, p = 0.03) than the control group. CONCLUSIONS Chest physical therapy as an adjunct to standard treatment does not hasten clinical resolution of children hospitalised with acute pneumonia and may prolong duration of coughing and rhonchi.