Objectives: Besides T- and B-cells also the innate immunity is playing an effective role in the pathogenesis of Juvenile idiopathic arthritis (JIA) reported in literature. The complement system (CS) is activated by the three different ways classical pathway (CP), lectin pathway (LP) and alternative pathway (AP). This is a controlled prospective observational single center study focused on the three pathways of CS and its effector, the terminal complement complex (TCC), associated with disease activity in all clinical JIA subgroups. Methods: Peripheral blood (PB) samples (n=159) of 60 JIA patients (partially also longitudinal visits) were analyzed for specific complement pathway activation (COMPL300 ELISA), complement factor H (CFH)-autoantibodies (CFHAb ELISA), and the soluble TCC (sC5b-9 ELISA) in serum (S) and EDTA plasma (P). TCC was also analyzed in synovial fluid (SF) of JIA patients (n=9) controlled with samples of healthy adults (n=12) obtained by arthroscopy (primarily gonarthrosis). As healthy controls (HC) adults (n=100) and children (n=18) without inflammatory diseases were tested. The JADAS10 defined the acute phase of the disease. Results: We compared the elevated serum TCC levels of JIA patients in the acute phase of the disease (13.32 IQR 8.09-19.48; p<0,001) with the controls' levels (7.78 IQR 4.93-10.31). Subgroup analyses showed statistically significant (s.s.) elevation in PArf+, OAper, and OAext. COMPL300 analyses revealed that JIA patients with acute disease had lower CP (82% IQR 37-97% vs 105% IQR 98-115%; p<0.001), LP (31% IQR 2-86% vs 80% IQR 20-101%; p<0.001), and AP (25% IQR 2-88% vs 85% IQR 70-98%; p<0.001) capacity compared to the HC average due to chronic activation in all three pathways. Both TCC and COMPL300 analyses during acute phase and remission showed a clear tendency, especially in PArf+ but only s.s. in the individual course. Remarkable sJIA patients neither in TCC nor in COMPL300 analyses showed complement activation. No evidence of CFH-autoantibodies was found in our study group. The TCC levels in SF showed a median of 2.48 IQR 1.71-2.76 AU/ml in JIA patients and surprisingly high levels in HC with 6.7 IQR 3.9-9.24 AU/ml. Conclusion: Specific subgroups of JIA patients (extOA, PARf+, ERA) showed increased CS activation in TCC in PB in the acute course of the disease. Furthermore, the decreased CS capacity, especially in the CP and AP, confirms the consumption of complement components as an additional contributor to the disease pathogenesis and acute course. Due to the CS activation throughout all disease activity states, we could not determine s.s. between the acute and remission phases in our cohort. However, COMPL300 in combination with TCC seems to be a helpful acute disease biomarker in the individual course. The pharmacological modulation of CS components might be a valid alternative approach in treatmentresistant patients, although further investigations are needed.