Patients with Shwachman-Diamond syndrome (SDS) have an increased frequency of myelodysplasia and leukemic transformation. We described two patients who received allogeneic stem cell transplantation and developed multiple complications, including seizure, hyperglycemia and renal tubular acidosis. A review of the literature showed that patients with SDS appeared to have an increased incidence of various transplant-associated problems. These patients frequently have underlying organ dysfunction and should be managed with extreme caution when treated with allogeneic stem cell transplantation.