To investigate whether a hospital-supervised program of chest physical therapy improves lung function in children with chronic pulmonary diseases, twenty-four children (4 with Kartagener?s syndrome, 12 with common variable immunodeficiency, and 8 with primary ciliary dyskinesia) average age 11.2 +/- 3.2 years, were randomly assigned to a one-month hospital-supervised program of chest physical therapy (13 patients) or to a control group (11 patients) that continued unsupervised chest physical therapy at home. Lung function was assessed before the program, and one and 12 months after. At the one-month assessment, thoracic gas volume was significantly lower in the supervised group than in the controls. At the one-year assessment, forced expiratory volume in one second was significantly higher in the supervised group than in controls. A supervised program of chest physical therapy significantly improved lung function in children with chronic pulmonary diseases.