Nutritional failure in children with cystic fibrosis (CF) has a negative effect on their morbidity and survival. It is unknown if determination of fat-free mass is a better screening method for nutritional failure than the currently recommended body mass index (BMI) alone. This cross-sectional study in 77 children with CF (age: 14.8±2.9y) measured fat-free mass, fat mass, bone mineral content and density using dual-energy X-ray absorptiometry. Nutritional failure was defined as BMI <10 percentile and/or fat-free mass index <5th percentile. Statistics were done using ANOVA and t-tests. Thirty-one percent (31%) of the patients with CF was characterized by nutritional failure, and 14% had low fat-free mass index with preserved values for BMI (hidden depletion). Only 52% of the patients with fat-free mass depletion was detected when using the criteria BMI <10 percentile. Patients with fat-free mass depletion had reduced values for forced expiratory volume in 1s (FEV(1)), independent of body mass index (P<0.05), and lower values for bone mineral density in whole body, spine and hip, and spine bone mineral apparent density (P<0.01). BMI ≤20 percentile was associated with a large drop in fat-free mass, a reduced FEV(1), and in bone mineral loss. Depletion of fat-free mass enhances morbidity in children with CF and is undetected in many of these children when only BMI percentile is used as screening method. BMI percentile of 20 should be considered as the new critical threshold for nutritional failure in CF if body composition techniques are not available.