Juvenile idiopathic arthritis (JIA) is a non-homogeneous autoimmune children's disease which, despite the applied therapy, has a progressive character with recurrences, leading to damage of joint structures. Progressive wearing of the joint cartilage in the course of JIA, which results from the imbalance between the biological strength of the cartilage, its function and exerted pressure forces, is linked to metabolic disorders of extracellular matrix (ECM) components. Among the latter compounds, the proteoglycan (PG) aggrecan plays a particular role in maintaining the mechanical-immunological properties of the cartilage. These functions are directly related to chains of glycosaminoglycans (GAGs), covalently linked to the core protein of PGs. Therefore, every change of GAGs metabolism linked to an increase of the rate of degradation or with a decrease of their biosynthesis may have pathological consequences. In this paper we aim to describe plausible mechanisms leading to observed disorders of aggrecan transformation in children, which are reflected in the profile of plasma GAGs. Therefore, we describe the plausible role of factors related to catabolism and synthesis of PGs/GAGs as well as the contribution of immunological processes to shaping the changes of extracellular matrix components in the course of JIA.