Hematopoietic cell transplantation is an important therapeutic option for many hematologic cancers. Kidney injury after hematopoietic cell transplantation often results from exposure to chemotherapy and radiation therapy, antibiotics, immunosuppressants, and the patient’s own immune system derangements. In these settings, organ toxicity frequently commences within the blood vessel’s innermost layer composed of specialized endothelial cells that have many unique roles in the body, including prevention of clot formation, maintenance of normal vascular tone, fluid filtration, and so on. Injury of endothelial cells in the kidney most often manifests as thrombotic microangiopathy, characterized by hemolysis, anemia, thrombocytopenia, proteinuria, and hypertension. Its pathological features include intracapillary thrombosis, fibrin deposition, mesangiolysis, and podocyte effacement. Kidney dysfunction is common in this population, and its prevention relies on early recognition of the problem and modification of supportive treatment that has grown increasingly complex over time and has outpaced our clinical diagnostic capabilities. Assessing endothelial dysfunction in patients undergoing hematopoietic cell transplantation with the application of novel research tools and methodologies may provide an opportunity for earlier recognition of organ toxicity and may ultimately improve patients’ outcomes.