Study design: Retrospective study Objectives: To compare the accuracy of estimated serum creatinine (Cre)-based glomerular filtration rates (eGFRcre) and serum cystatin C (CysC)-based eGFR (eGFRcys) for determining renal function in patients with spinal cord injury (SCI). Setting: Department of Urology, Tohoku Rosai Hospital, Japan Methods: Male patients with SCI for longer than 5 years after injury were eligible for inclusion in this study. eGFRcre and eGFRcys were calculated using the following formulas: eGFRcre = 194 × Cre-1.094 × age-0.287; eGFRcys = (104 × CysC-0.1019 × 0.996age)-8. The eGFRcre/eGFRcys ratio between 0.8 and 1.2 was considered to be equal, and a relationship between them was investigated. Demographic data, degree of spinal cord damage, management of bladder emptying, post-injury period, and ambulatory status were evaluated. Results: A total of 115 male patients were included. eGFRcre overestimated renal function in 87 (76%) patients with SCI compared with eGFRcys. On univariate analysis, renal function by eGFRcre was overestimated in patients with an eGFRcre of more than 60 ml min-1 per 1.73 m2 (P < 0.001), in non-ambulatory patients (P < 0.001) and, in patients with complete paralysis (P < 0.001). On multivariate analysis, an eGFRcre of more than 60 ml min-1 per 1.73 m2 (P < 0.001), non-ambulatory status (P < 0.001), complete paralysis (P = 0.17), and age (P < 0.001) were independent factors for overestimated renal function by eGFRcre. Conclusions: eGFRcre overestimates renal function compared with eGFRcys. eGFRcys is beneficial, particularly in patients with an eGFRcre of more than 60 ml min-1 per 1.73 m2, in non-ambulatory patients, and in older patients with SCI.