Background & aims: little is known about the impact of disease and treatment on the pattern of growth in children with Inflammatory Bowel Disease (IBD). Significant deficits in height and weight in children with Crohn’s disease have been reported but changes in fat and fat free mass are less well defined. This study aims to describe the height, weight and body composition of a cohort of children with IBD. Methods: height, weight, skinfold thicknesses and bioelectrical impedance analysis was performed. Disease activity was assessed with clinical scoring systems. Results: 55 children, median age 13.7 years (range 6.5–17.7) were studied. Median (25th, 75th percentile) Standard Deviation Score for BMI, Height and Weight were − 0.3 (− 0.97, 0.65), − 0.56 (− 1.42, 0.06), − 0.62 (− 1.43, 0.19). In Crohn’s disease, using multiple regression analysis disease activity measured by PCDAI was significantly inversely related to fat free mass (β − 0.2, 95% CI −0.17, −0.03, p 0.005). Conclusions: children with IBD were both under and overweight. Nutritional deficits were more common in Crohn’s disease. Fat free mass was related to disease activity in children with Crohn’s disease regardless of changes in weight. Weight or BMI may mask deficits in lean tissue in the presence of normal or increased proportions of body fat.