Calcineurin inhibitors (CNI), cyclosporine and tacrolimus, are commonly used for pharmacotherapeutic prophylaxis of Graft-vs.-Host disease after hematopoietic cell transplantation (HCT). Unfortunately, their use is associated with significant toxicities. While intolerance to CNI is well defined, there is very little data on how they impact outcomes after HCT in children. Our retrospective study in a cohort of 82 children, shows a high intolerance rate of 39% in this population associated with lower event free survival and a higher transplant-related mortality.