We retrospectively reviewed the medical records of 75 allogeneic hematopoietic transplant recipients and evaluated cystatin C as a potential marker of subsequent renal dysfunction. Acute kidney injury developed in 31 of 75 patients after a median of 46 days post-transplantation (range 1-502 days), while worsening of chronic kidney disease (CKD) was observed in 21 patients during the observational period. Cystatin C level was significantly elevated after allogeneic transplantation (P < 0.001). Multivariate analysis revealed the use of calcineurin inhibitors as a major cause of cystatin C elevation (odds ratio 7.26, P = 0.04). A strong inverse correlation was also noted between cystatin C and estimated glomerular filtration rate (r = -0.682, P < 0.001). Cystatin C measurement could provide a useful clinical tool to identify hematopoietic stem cell transplantation recipients at an increased risk for CKD.