Background: With the widespread use of hematopoietic stem cell transplantation (HSCT), long-term complications have come to the fore. The aim of this study is to determine the prevalence and risk factors of chronic kidney disease (CKD) developing in the long term in patients who underwent allogeneic HSCT in childhood and also to investigate the superiority of eGFR formulas. Methods: The present study evaluated CKD in patients undergoing allogeneic HSCT. We analyzed the 94 children who received allogeneic HSCT at the Ege University in İzmir between 2019 August and 2019 November. The patients were evaluated at least 2 years after transplantation. CKD was defined as a glomerular filtration rate (GFR)<90 mL/min/1.73 m2, using eGFR equations which are based on serum creatinine (SCr), cystatin C (CysC), and SCr plus CysC. Results: In our study, 9 (9.4%) according to Bedside Schwartz, 59 (76.6%) according to CKiD-eGFR-CysC and 20 (26%) patients according to CKiD-eGFR-SCr-CysC equation were evaluated as CKD. In cases evaluated as CKD according to CysC, early development of acute kidney injury (AKI), posttransplant cytomegalovirus (CMV) reactivation and being >10 years old during transplantation were found to be associated with the development of CKD. Conclusion: We may be delayed in detecting CKD by calculating SCr-based formulas in HSCT cases, which is a patient group where early diagnosis and treatment of CKD is very important.