We report a high incidence (19.5%) of autoimmune hemolytic anemia (AIHA) in 41 patients with SCID who underwent a T cell-depleted haploidentical transplant. Other than infections, AIHA was the most common post-transplant complication in this patient cohort. Clinical characteristics and treatment of eight patients who developed AIHA at a median of 8 months after the first T cell-depleted transplant are presented. All patients had warm-reacting autoantibodies, and two of eight had concurrent cold and warm autoantibodies. Clinical course was most severe in two patients who had cold and warm autoantibodies. Five patients received specific therapy for AIHA. Successful taper off immunosuppressive therapy for AIHA coincided with T cell reconstitution. Delayed reconstitution of T cell immunity, due to T cell depletion, immunosuppressive conditioning and CsA, as well as paucity of regulatory T cells, are the likely explanations for the occurrence of AIHA in our patient cohort. Screening of the population at risk may prevent morbidity and mortality from AIHA.