Juvenile idiopathic arthritis (JIA) is one of the most common chronic inflammatory diseases occurring in childhood, associated with decreased bone mineral density (BMD) and increased risk of osteopenia and osteoporosis, which increases the fracture risk. Aim of the work: to assess BMD and bone turnover markers (serum osteocalcin for bone formation and C terminal telopeptide of type 1 collagen for bone resorption) in JIA patients and their relation to disease activity. This study included 50 patients with JIA (female:male – 20:30). The study was approved by the Ethical Research Committee and Institutional Review Board of the Faculty of Medicine, Menoufia University, Egypt (Approval number: 19519INTPH48). Written informed consent was obtained from each patient or the parents. These patients were diagnosed with JIA according to the criteria of classification of the International League of Associations for Rheumatology. BMD was measured by Dual-energy X-ray absorptiometry (DEXA) of the lumbar spine using the Z-score. The results were correlated with JIA disease duration, disease activity, bone turnover markers and serum level of vitamin D. Clinical disease activity was evaluated by juvenile arthritis disease activity score (JADAS-27). There was a significant negative correlation between DEXA Z-score and disease activity (p-value < 0.001), bone turnover markers (p-value < 0.001), and duration of JIA (p-value < 0.05). There was a significant difference between vitamin D level and DEXA Z-score; DEXA Z-score was lower in vitamin D deficient patients. JIA patients with higher disease activity are at a higher risk of osteopenia and osteoporosis. Well-timed and efficient treatment of JIA and proper control of disease activity may help to improve the bone status and reduce the incidence of osteoporosis. Consequently, valuable targeted interventions are essential to preserve bone health during JIA.