Hematopoietic stem cell transplantation (HSCT) exposes a patient's kidneys to a unique combination of challenges, including high-dose radiation, anemia, chemotherapeutic agents, graft-versus-host disease, opportunistic infections, attenuated and altered immunologic responses, fluid and electrolyte imbalances, and extensive courses of antimicrobial agents. Since the inception of HSCT in the 1950s, there has been increasing interest in defining, determining, and managing the kidney complications that accompany this procedure. In this article, we review the common causes of acute kidney injury and chronic kidney disease that occur with HSCT, including HSCT-associated thrombotic microangiopathy, a distinct cause of chronic kidney disease with a multifactorial cause previously known as bone marrow transplant nephropathy or radiation nephropathy. Additionally, we review other kidney complications, including calcineurin inhibitor nephrotoxicity and chronic graft-versus-host disease-associated glomerulonephritis, that develop post-HSCT. Critically, due to its grave prognosis, it is important to identify HSCT-associated thrombotic microangiopathy early, as well as distinguish it from the other causes of chronic kidney disease.