The search for biomarkers in paediatric rheumatic diseases, particularly juvenile idiopathic arthritis (JIA), childhood lupus nephritis (LN), and juvenile idiopathic inflammatory myopathies (JIIMs) is attracting increased interest. In JIA, a number of biomarkers have shown potential for predicting clinical phenotype, disease activity and severity, clinical remission and relapse, response to treatment, and disease course over time. In systemic JIA, measurement of biomarkers that reflect the degree of activation and expansion of T cells and macrophages might be helpful for detecting subclinical macrophage activation syndrome. Urine biomarkers for childhood LN hold promise for facilitating early diagnosis and improving disease monitoring and assessment of response to therapy. Myositis-specific autoantibodies define distinct serological subgroups of JIIMs, albeit with similar clinical features, responses to therapy, and prognoses. Use of biomarkers may potentially help to avoid invasive procedures, such as renal biopsy in systemic lupus erythematosus and muscle biopsy in juvenile dermatomyositis. Incorporation of effective and reliable biomarkers into routine practice might facilitate adoption of a stratified approach to investigation and management, foster the implementation of research into the design of personalized and targeted therapies, and ultimately lead to more rational and effective clinical care.