Hematopoietic Cell Transplantation (HCT) frequently results in kidney dysfunction, which has been shown to have a detrimental effect on both short and long term mortality. This complication has numerous, frequently overlapping, and poorly understood causes. Management therefore calls for multifaceted research and concurrent treatment of potential causes. Due to a lack of precise markers and the high prevalence of renal biopsy contraindications among HCT recipients, the etiology is typically left unexplained. Here, we offer a synopsis of the pathogenesis and suggest an approach for assessing kidney damage following HCT. We also identify the most critical research directions that should be pursued in order to identify people at risk for severe renal injury and create nephroprotective measures.