Hematopoietic stem cell transplantation (SCT) recipients are exposed to a large amount of anti-cancer drugs, immunosuppressors, and irradiation during the peri-SCT period. Thus, they have to overcome serious adverse events related to unavoidable but toxic procedures, including organ disorders. In particular, acute kidney injury (AKI) is one of the most critical complications, because it influences the mortality of patients. A few patients who survive AKI may develop nephrotic syndrome, and precedent AKI is also closely associated with chronic and progressive loss of the renal function in post-SCT patients. These kidney diseases place a heavy burden on SCT patients, both medically and economically. Therefore, hematologists who evaluate SCT should be fully aware of the development of these kidney diseases after SCT. We herein review the common course of kidney disease development following allogeneic SCT to provide healthcare professionals with practical information on renal disease in SCT patients.