The advent of biologic disease-modifying antirheumatic drugs targeting specific cytokines or cell-cell interactions has dramatically changed the outlook of patients with juvenile idiopathic arthritis. However, safety concerns remain around the use of therapeutic agents for children with juvenile idiopathic arthritis. Foremost among these are the risks of serious infections and malignancy. This article provides an overview of methodologies for pharmacosurveillance in juvenile idiopathic arthritis, including spontaneous reporting systems and the use of diverse data sources, such as electronic health records, administrative claims, and clinical registries. The risks of infections and malignancies are then briefly reviewed.