Novel therapies including biologic agents offer paediatric rheumatologists significant opportunity to improve long-term prognosis for children with rheumatic disease. However, comorbidities related to the diseases themselves and their treatments pose specific challenges to be overcome. Prompt recognition and appropriate management will improve quality of life, effectiveness of treatment and overall prognosis. In this review, we discuss key areas of comorbidity frequently encountered in paediatric rheumatology including cardiovascular, renal, genito-urinary and visual comorbidity, bone health, drug-related issues and the influence of rheumatic disease on growth and puberty.