In all subgroups of juvenile idiopathic arthritis, a decrease in bone mass has been described in a high percentage of children. Recently, new pathogenetic concepts have identified muscle mass as the strongest predictor of bone mass and bone is now recognized as part of the musculoskeletal system. In addition, the sophisticated use of bone densitometry in pediatrics, including new measurement techniques, has provided the tools for a reliable assessment. A standardized diagnostic approach to the musculoskeletal system, including prophylaxis and therapy, is, therefore, mandatory in all children with JIA who do not achieve rapid remission. In this review, diagnostic and therapeutic options are being described and possibilities to incorporate them into clinical practice are suggested.