The evaluation of split kidney function is of clinical significance for patients after renal transplantation. This study explored two available approaches, dynamic MR renography vs. 99mTc-DTPA clearance, for determining split renal GFR in 57 transplanted patients. MR-based GFR was measured using an established Baumann-Rudin model, modified two-compartment and three-compartment model. MR results were compared with 99mTc-DTPA, using 24-h creatinine clearance rate as a reference. MRR using a 2C model had significantly higher accuracy (r = 0.925) than 99mTc-DTPA clearance (r = 0.317), thus could be a more promising way for evaluation of transplanted kidney function.