Many conditions can cause or be associated with arthritis in childhood. The authors of this paper will review the situations in which underlying immunodeficiency or defective regulation of lymphocyte homeostasis must be suspected, and discuss, for some of these diseases, the genetic bases and pathogenesis. In the second part of this article, the authors will focus on other diseases that can cause arthritis in childhood, often with other symptoms, and for which evidence of an association with genetic abnormalities has been recently discovered. Finally, the authors will discuss the implications of recent findings regarding the role of some genes as causing or modulating factors in juvenile idiopathic arthritis and related disorders, as well as observations made in adults and in animal models of inflammation and autoimmunity.