Chronic Kidney Disease (CKD) is a serious complication of methylmalonic acidemia (MMA), manifests with proximal tubular dysfunction, tubulointerstitial nephritis, and eventually decreased glomerular filtration. Routine diagnostic tests, like serum creatinine, leave much to be desired. In this study, we designed an alternative MRI strategy to measure renal perfusion and create pH maps after administering iopamidol, a pH sensitive contrast agent. We detected robust differences in perfusion fraction and pH maps between severe, mild and no renal disease in MMA mouse model. These results demonstrate that MRI may facilitate early detection of kidney disease.