Abstract Elucidating the molecular mechanisms of immunodeficiency diseases is a powerful approach to discovering new immunoregulatory pathways in humans. One such previously unknown pathway is that of GIMAP5, an evolutionarily conserved GTPase expressed in T and NK lymphocytes, also known as the gene mutated in the Biobreeding diabetic rat and Sphinx lymphopenic mice. To better understand this disease association, we identified causative GIMAP5 mutations in 17 individuals of 9 kindreds with lymphopenia, liver disease, splenomegaly, thrombocytopenia, lymphadenopathy, lung infections, and lymphoma. As the mechanism of action, we now report that GIMAP5 controls the pathological accumulation of long chain ceramides. The ceramide synthase inhibitor, fumonisin B1, rescues GIMAP5-deficient T cells from ceramide overaccumulation and cell deterioration. Concordant with these findings, induction of ceramide accumulation and cell death by exogenous C6-ceramides in human T cell blasts was reduced by fumonisin B1 and GIMAP5 overexpression. Our work reveals the underlying long-chain ceramide mechanics of GIMAP5, opening new opportunities for further metabolomic studies of immunodeficiency diseases and targets for the development of therapeutics. This research was supported by NIAID by the Intramural Research Program of the NIH.