In recent years the treatment of juvenile idiopathic arthritis (JIA) has changed dramatically. Nowadays one out of three children with polyarticular JIA is treated with a biologic drug; however, knowledge about the long-term safety of biologics is still limited. Information on drug safety is collected in the JIA biologic register (BiKeR) and the follow-up register juvenile arthritis methotrexate/biologics long-term observation (JuMBO). The latter currently includes information on more than 700 young adults most of whom were treated with etanercept and prospectively followed for more than 5 years. Preliminary data on the long-term safety of etanercept for JIA are therefore available. Over an observation period of 1,800 etanercept exposure-years, events of particular interest, such as malignancies, serious infections and new onset immune-mediated diseases have been recorded which occurred at rates of 0.1, 1.1 and 0.9/100 patient-years, respectively. Overall, new safety risks were not detected during long-term etanercept exposure. Moreover, JuMBO has also provided information on the long-term outcome of JIA and initial evidence suggests that JIA outcome, especially in functional aspects has improved in the biologic era. Data from BiKeR and JuMBO contribute to the risk-benefit assessment of biologic drugs which have been implemented in the routine treatment of JIA.