Several genetic factors have recently been observed as having an influence on susceptibility, course and prognosis of juvenile idiopathic arthritis (JIA): 1. Affected sib pairs were observed to have a low concordance in terms of disease incidence, but significant concordance in terms of subtype and course of disease. 2. Each subtype of JIA was observed to have a distinct genetic background. 3. Some JIA patients do not carry any of the defined risk genes. 4. Most subtypes of JIA have a distinct different genetic background to rheumatoid arthritis in adults. 5. Multiple factors have been observed to be involved in pathogenesis implying genetic and environmental factors. 6. Systemic JIA differs from all other subtypes in terms of genetic background and treatment options. It is currently assumed to be an autoinflammatory disease. 7. Genetic factors not only affect the course of the disease, but also response and complication rate. Increasing knowledge on the factors involved in the pathogenesis of JIA as well as analysis of large patient cohorts in consortiums cooperating on an international level have helped define many important polymorphisms; these are currently the subject of further investigation.