The objective of this study was to determine the relationship in regional cerebral blood flow (rCBF) as measured with perfusion magnetic resonance imaging (pMRI) and single photon emission computer tomography (SPECT). rCBF was determined in 26 healthy subjects with pMRI and SPECT. After co-registration of pMRI with SPECT, rCBF was determined in 10 brain regions relative to the whole slice value. pMRI was evaluated with and without elimination of large vessels. rCBF from pMRI correlates significantly with rCBF from SPECT (r = 0.69 with and r = 0.59 without elimination of large vessels; p < 0.0001 for both). Elimination of large vessels reduced the interindividual variance of the pMRI measurements in most regions. rCBF from pMRI shows good correlation with rCBF from SPECT. Because pMRI is sensitive to flow in large vessels while SPECT is not, elimination of large vessels in pMRI reduces the interindividual variability of pMRI and improves the-correlation between the two methods. pMRI is a reliable noninvasive method for rCBF measurements.