Chronic kidney disease is common in pediatric patients following hematopoietic stem cell transplant. Its etiology is likely multifactorial and depends both on pre-conditioning regimens as well as immunosuppressive therapy and posttransplant prophylactic medications. Graft vs. host disease (GVHD) is a common sequela of hematopoietic stem cell transplant and has been associated with the nephrotic syndrome (NS). Here we report a case of a pediatric patient who developed proteinuria and renal insufficiency after stem cell transplant. A kidney biopsy showed chronic interstitial nephritis and extensive foot process effacement, which are likely sequelae of GVHD. Moreover we show decreased CD4 and CD3 lymphocyte counts in the interstitial infiltrate, suggesting that abnormal lymphocyte response might play a role in podocyte injury following GVHD. This case illustrates the importance of the kidney biopsy in the assessment of stem cell transplant-mediated renal failure.