The purpose of this study was to determine the accuracy and sources of error in estimating single kidney glomerular filtration rate (SKGFR) derived from low-dose gadolinium-enhanced T1-weighted MR renography. To analyze imaging data, MR signal intensity curves were converted to concentration versus time curves and a three-compartment, six-parameter model of the vascular nephron system was used to analyze measured aortic, cortical and medullary enhancement curves. Reliability of the parameter estimates was evaluated by sensitivity analysis and by performing Monte Carlo analyses of model solutions to which random noise had been added. The dominant sensitivity of the medullary enhancement curve to GFR during a 1 - 4 min window following tracer injection was supported by a low coefficient of variation in model-fit GFR values (4%) when measured data were subject to 5% noise. These analyses also showed the minimal effects of bolus dispersion in the aorta and differences in GFR on parameter reliability. Single kidney GFR from MR renography analyzed by the multicompartmental model ranged from 4.0 to 71.4 ml/min and agreed well with reference measurements using ^99mTc-DTPA clearance and scintigraphy (r = 0.84, p < 0.001). Bland-Altman analysis found an average difference between model and reference values of 11.9 ml/min (95% confidence interval, 5.8 - 17.9 ml/min).We conclude that a nephron-based multicompartmental model can be used to derive clinically useful estimates of single kidney GFR from low dose MR renography.