Reduced bone mineral density (BMD) has been reported in adults with Crohn's disease (CD). Less is known about abnormal BMD in children and young adults with CD. The aims of this study are to determine the prevalence of low BMD and to evaluate the effect of growth and pubertal development on BMD in children and young adults with CD. One hundred-nineteen patients with CD underwent dual-energy X-ray absorptiometry (DXA) to determine BMD. Anthropometry and pubertal development were measured. Bone age was measured only in patients older than 8 years of age and who had not grown in height during the last year. One hundred-nineteen patients (72 male, 47 female) were evaluated. Seventy percent of patients had BMD z-scores ± −1.0 and 32% had z-scores ± −2.0. Weight and height z-scores were significantly associated with BMD z-scores. BMD z-scores based on bone age and on chronological age were highly correlated, except when the chronological age BMD z-score was ± −2.0. BMD z-score was significantly different between males and females for the group (–1.75 ± 1.06 vs. −1.08 ± 1.00), respectively. Children and young adults with CD have a high prevalence of low BMD and routine evaluation by DXA is indicated. In patients with a chronological age-based BMD z-score ± −2.0, a bone agebased BMD should be considered.