In the last years, the interest in the concept of comorbidity and its societal as well as individual impact has increased. Juvenile idiopathic arthritis (JIA) is a chronic inflammatory disease starting in childhood which often persists into adulthood. Clinicians are facing an aging population with multiple morbid conditions occurring in one individual. Long-term outcome studies show the high prevalence and the potential interaction of co-existing diseases. For JIA recent studies reported that uveitis, asthma/atopic diseases, and diabetes mellitus are prevalent comorbidities in JIA with 11.6–30%, 10.8%, and 3.5%, respectively, followed by cardiovascular disease, malignancies, and inflammatory bowel diseases. Also in childhood, long-term outcome studies and registries might reveal associations of co-existing diseases and medication used. The impact of comorbidity on the patient’s overall well-being should be taken into account. It is important to plan preventive and screening strategies in order to prevent or early detect and treat comorbidities and integrated follow-up once comorbidity exists.