Kidney dysfunction is a common complication of hematopoietic cell transplantation (HCT) with proven negative impact on early and long-term mortality. Causes of this complication are diverse, usually overlapping, and poorly understood. Therefore, management implicates multidirectional investigations and simultaneous treatment of suspected causes. The etiology is frequently unconfirmed due to a lack of specific markers and prevalence of contraindications to renal biopsy among HCT recipients. Herein, we provide a summary of etiology and propose an algorithm for evaluation of kidney injury after HCT. We also map out the most urgent areas for research that aim to identify patients at risk of severe renal injury and develop nephroprotective strategies.