The aim of this study was to evaluate the association of circulating cartilage oligomeric matrix protein (COMP) and human cartilage glycoprotein-39 (YKL-40) as markers of metabolic changes of cartilage, with leptin, adiponectin, and resistin in juvenile idiopathic arthritis (JIA) patients before and after treatment. A significant decrease of COMP and an increase of YKL-4 were found in blood of untreated patients. JIA treatment leading to clinical improvement resulted in normalization of COMP levels only. Concentrations of both markers in treated patients, while showing no clinical improvement, differed from those in controls and patients with remission. The leptin level decreased (p < 0.05) in untreated patients; however, concentrations of adiponectin and resistin increased (p < 0.05) as compared to controls. JIA treatment resulted in normalization of adipocytokine levels in remissive patients but not those with active JIA. Untreated patients showed a correlation between COMP and leptin, adiponectin, and body mass index (BMI) and between YKL-40 and leptin, adiponectin, BMI, C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR). In inactive JIA, a correlation between YKL-40 and leptin was shown. Treated patients with an active JIA demonstrated a correlation between COMP and adiponectin and between YKL-40 and leptin, adiponectin, BMI, CRP, and ESR. The results of this work indicate that leptin and adiponectin but not resistin may be involved in the development and progression of joint dysfunction in JIA. Additionally, we suggest that YKL-40 may be a useful biomarker of disease activity and may be used to assess treatment towards remission, as compared to COMP.Metabolites 2020, 10, 61 2 of 11 remodeling, manifested by significant changes of the circulating markers of cartilage turnover, including total glycosaminoglycans (GAGs) and their particular types such as keratan sulphate, chondroitin sulphate, hyaluronic acid, as well as chondroitin sulphate 846 epitope [5][6][7][8].Among ECM components, which are indicators of the cartilage breakdown, there are also listed components synthesized by chondrocytes, i.e., cartilage oligomeric matrix protein (COMP) as well as human cartilage glycoprotein 39 (YKL-40), that are so far not evaluated in JIA patients. The first one is a non-collagenous glycoprotein, binding to aggrecan; fibronectin; and collagen types I, II, and IX, which seem to play a role in the structure of fibrils and in maintenance of the collagen network [9,10]. Whereas YKL-40, a glycoprotein associated with inflammation and tissue remodeling, is produced by joint tissues and recognized as a candidate autoantigen in rheumatoid arthritis. It has been shown that YKL-40 binds to some important components in the cartilage extracellular matrix, i.e., proteoglycans and collagens, influencing their production and assembly [11][12][13][14]. Several authors have investigated the relationship between circulating COMP or YKL-40 and the condition of articular cartilage in adult patients with and without any r...