OBJECTIVE\nTo evaluate interactions between skeleton and adipose tissue, and association of adipokines and bone turnover markers with disease-related factors in patients with severe juvenile idiopathic arthritis (JIA).\nMETHODS\nForty-nine patients (median age 14.8 yrs, median disease duration 10.2 yrs) with refractory polyarticular JIA and 89 sex-matched and age-matched healthy controls participated in the study. Study subjects underwent clinical examination, body composition assessment with dual-energy X-ray absorptiometry, and analyses for leptin, adiponectin, and bone turnover markers.\nRESULTS\nPatients with JIA were shorter and more often overweight (p = 0.001) or obese (p < 0.001) than controls. They had significantly higher serum leptin, even when adjusted for fat mass (p < 0.001), than did controls. Adiponectin did not differ between the groups. Concentration of carboxyterminal telopeptide of type I collagen was higher (p = 0.006) in patients. The inverse association between leptin and bone turnover markers disappeared in controls but was strengthened in patients when adjusted for fat mass. Leptin, adiponectin, or bone markers did not associate with variables of disease activity.\nCONCLUSION\nPatients with severe JIA had high adiposity accompanied by increased bone resorption. Their serum leptin was higher, even independently of fat mass. Leptin tended to associate inversely with bone turnover markers but did not associate with variables of disease activity.