A retrospective audit was conducted in 1998 and 2000 to review the physiotherapy management of hospitalized children with cystic fibrosis (CF) at the Brisbane Royal Children's Hospital (RCH). The objective was to detect and explore possible changes in patient management in this time period and investigate whether these changes reflected changes in the current theory of CF management. All children over two years of age with CF admitted during 1998 and 2000 with pulmonary manifestation and who satisfied set criteria were included (n = 249). Relative frequency of each of six treatment modalities used were examined on two occasions, revealing some degree of change in practice reflecting the changes in current theory. There was a significant decrease in the frequency of usage of postural drainage with head-down tilt (p < 0.001), and autogenic drainage (p < 0.001) between 1998 and 2000. Modified postural drainage without head-down tilt (p < 0.001), and positive expiratory pressure devices (p < 0.001) were used more frequently in 2000 (p < 0.001). No significant changes were identified in the use of Flutter VRP1 (p = 0.145) and exercise (p = 0.763). No significant differences were found in population demographics or occurrence of concomitant factors that may influence patient management.