Despite our current treatment, many cystic fibrosis (CF) patients still show progressive bronchiectasis and small airways disease. Adequate detection and monitoring of progression of these structural abnormalities is needed to personalize treatment to the severity of CF lung disease of the patient. Chest computed tomography (CT) is the gold standard to diagnose and monitor bronchiectasis. Many studies have been done to validate the role of chest CT in CF and to improve the protocols. From these studies it became clear that for correct interpretation of the severity of bronchiectasis and small airways disease standardization of lung volume for the inspiratory and expiratory CT scan acquisition is needed. The risk related to the radiation exposure of a chest CT scan every second year is considered low. Automated and quantitative image analysis systems are developed to improve the reliability and sensitivity of assessments of structural lung changes in CF, particularly in early life. In this paper an overview is given of the lessons learned from two decades of monitoring CF lung disease using chest CT.