​The exact causes of JIA are unknown. In certain arthritis, the malfunctioning of body's immune system may be due to a trigger such as a viral infection which can set off the condition.

Like other autoimmune diseases, JIA may be linked to genetic factors associated with an abnormal immune response. A family history of JIA and / or other autoimmune diseases are risk factors, but there is no precise way of predicting how high the risk is if there is an affected member in the family.