Hematopoietic stem cell transplantation, autologous or allogeneic, is a well established hematology procedure. There can be a number of renal complications in this setting, which may occur in every phase but all strongly influence prognosis. Among the late complications, there is the well-known possibility of progressive chronic renal failure, appearing together with hypertension and modest alterations of the urinary sediment, and characterized by pathological findings of thrombotic microangiopathy, often without the corresponding clinical aspects. This clinical picture must be distinguished from other forms of clinically more severe thrombotic microangiopathy, such as those occurring in the early post-transplant period, and from other causes of renal disease in the hematopoietic stem cell transplantation setting. Total body irradiation, chemotherapeutic drugs, calcineurin inhibitors and opportunistic infections have all been considered as causal factors. The nosological classification is still poorly defined, as are the real prognosis and the best treatment. Kidney biopsy is a necessary tool to make a correct diagnosis, assess the frequency of the condition, make a prognostic judgment, and set up rational treatment.