FOXP3 is the key mediator of regulatory T-cell development in the thymus. Naturally occurring mutations of FOXP3 interfere with this process, resulting in the generation of autoaggressive lymphocyte clones that are directly responsible for the syndrome Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked (IPEX) in humans and scurfy in mice. Stem cell transplantation is the only cure for IPEX patients. The study of this rare disease has provided important insight into the mechanisms of immunosuppression, autoimmunity and tolerance and future studies may lead to novel strategies to treat not only patients with IPEX, but also those suffering from autoimmunity, graft-versus-host disease or cancer.