In children with inflammatory bowel disease, controversy continues about the use of long-term alternate day prednisone therapy (ADP) to suppress disease activity and to encourage appetite and growth. One possible side effect of both disease process and prednisone therapy is risk of development of osteoporosis. To evaluate this risk factor, growth, biochemical indices of mineral and vitamin D status, and bone mass were measured in nine adolescents with Crohn's disease (CD) who were treated with ADP (0.3 mg/kg > 3 months per year) compared with eight adolescents treated with minimal ADP exposure (< 3 months per year). Single photon densitometry was used to measure bone mineral mass at the 1/3 distal radius three times over 2 years. Mean age of the 17 CD boys was 13.9 +/- 2.1 years at baseline. CD patients had lower bone BMC/BW mineral content/bone width (BMC/BW) compared with age- and height-matched normal boys at all times. The difference was less when compared to height-matched normal values as CD patients were shorter than healthy reference boys. Plasma 1,25-dihydroxyvitamin D, alkaline phosphatase, and parathyroid hormone significantly increased with treatment of disease but there were no differences between treatment groups. CD patients treated with ADP had similar heights and weights at baseline and demonstrated similar linear growth over 2 years (9.1 cm/2 years) to CD patients without ADP (10.3 cm/2 years). In both groups, BMC/BW increased significantly from year 1 to year 2, but absolute values for bone mass did not differ between the groups.