To compare visceral adipose tissue (VAT) mass, lipid profile, and selected adipokines/cytokines in patients with juvenile idiopathic arthritis (JIA) with controls, and to explore associations between these markers and VAT. We included 60 JIA patients (30 oligoarticular,30 polyarticular), aged 10-16 years, and 60 age-and sex-matched controls. VAT (g) was estimated by dual-energy x-ray absorptiometry. Lipid profile and selected adipokines/cytokines were analyzed by standard methods and ELISA, respectively. VAT (g) was comparable between patients and controls [median (25th-75th percentile): 64 (23-149) g vs. 66 (30-99) g, p = 0.98] and between oligoarticular and polyarticular disease courses [46 (22-123) g vs. 80 (23-167) g, p = 0.32]. Patients had lower serum levels of apolipoprotein A1 (APOA1) and elevated levels of interleukin- 6 (IL-6) and progranulin compared to controls. As compared to oligoarticular disease course, patients with polyarticular disease had lower serum levels of low-density lipoprotein cholesterol (LDL-C), lipoprotein(a) (Lp(a)), interleukin 1 receptor antagonist (IL-1RA) and progranulin, and elevated levels of interleukin-1 beta (IL-1b) and IL-1b/IL-1RA ratio. In patients (B, 95% CI), higher IL-6 (48.7, 25.1 to72.2, p <
0.001), resistin (8.5, 5.1 to 11.8, p <
0.001), and leptin (2.5, 0.9 to 4.0, p = 0.002) were associated with higher VAT. In controls, higher leptin (5.3, 3.7 to 6.9), p <
0.001) was associated with higher VAT. Despite similar VAT mass between patients and controls, VAT was related to IL-6 and resistin in patients only, suggesting an active metabolic role in JIA. Several pro-inflammatory adipokines/cytokines were increased in JIA, with differences in Lp(a) between oligoarticular and polyarticular disease courses.