The objective of this study was to examine the effects of a supervised exercise training program performed during an in patient rehabilitation course on various attributes of health-related fitness, e.g., flexibility, balance and coordination. 286 patients with CF, age range 6-18 years (11.8 +/- 3.4 years), mean forced expiratory volume in 1 sec (FEV1 82.7 +/- 22.3% predicted) were included. Patients performed the modified Munich fitness test (mMFT) to assess flexibility, balance, strength and coordination. To assess aerobic capacity a 6-min walk-test (6MWT) was performed. In addition, some of the patients performed an incremental exercise test on a bicycle ergometer using the Godfrey protocol before and after the exercise training program. The supervised training program consisted of 4-6 weeks of different sports activities 5 times per week. After training, pulmonary function showed a significant (P < 0.05) increase. All test items of the mMFT improved significantly (P < 0.05). Compared to healthy children test scores achieved from children with CIF in the mMFT were lower but within a normal range. Our children with CIF had a lower walk distance in 6MWT (P < 0.05) compared to healthy. Our findings clearly demonstrated benefits of a systematic exercise training program on components of physical fitness in patients with CE with improvements of test-tasks to predicted normal in some cases. The results from our study suggested that an exercise training program in CIF should be focused on several aspects of physical fitness including all components of physical fitness, e.g. aerobic endurance, flexibility, balance and motor skills.