Recipients of hematopoietic cell transplantation may be at risk for developing acute kidney injury and this risk may increase in patients who undergo transplantation for severe systemic sclerosis due to underlying scleroderma renal disease. Acute kidney injury after transplantation can increase transplant related mortality. To better define these risks, we analyzed 91 patients with systemic sclerosis who were enrolled in three clinical trials in the United States of autologous or allogeneic hematopoietic cell transplantation. Eleven (12%) of the 91 scleroderma patients in these studies (8 autologous, 1 allogeneic, 1 pre-transplant, 1 given intravenous cyclophosphamide on transplant trial) experienced acute kidney injury of whom eight required dialysis and/or total plasma exchange. Acute kidney injury in the 9 transplant recipients developed a median of 35 (range, 0–90) days after transplantation. Ten of 11 patients with acute kidney injury received angiotensin converting enzyme-inhibitors (ACE-I) treatment. The etiology of acute kidney injury was attributed to scleroderma renal crisis in 6 patients (including two with normotensive renal crisis), acute kidney injury of uncertain etiology in 2 patients and acute kidney injury superimposed on scleroderma kidney disease in 3 patients. Eight of the 11 patients died: causes of death included progression of SSc (1), multiorgan failure (1), gastrointestinal and pulmonary bleeding (1), pericardial tamponade and pulmonary complications (1), diffuse alveolar hemorrhage (1), pulmonary embolism (1), graft-versus-host disease (1) and malignancy (1). Limiting nephrotoxins, cautious use of corticosteroids, renal shielding during total body irradiation, strict control of blood pressure and aggressive use of ACE-I may be of importance in preventing renal complications after hematopoietic cell transplantation for systemic sclerosis.