Haploidentical hematopoietic stem cell transplant with T-cell depletion may result in donor T-cell engraftment in infants with severe combined immunodeficiency disease. Engraftment of other hematopoietic lines is achieved rarely, and pancytopenia and hemophagocytosis as a result of donor T-cell engraftment have not been reported. We report an infant with severe combined immunodeficiency who developed graft versus host disease with pancytopenia as a result of engraftment of maternal T cells after T-depleted hematopoietic stem cell transplant. His pancytopenia resolved after thymoglobulin and a stem cell boost. Thrombocytopenia resolved with rituximab.