We hypothesized that myocardial perfusion imaging (MPI) would fail to identify all vascular zones with the potential for myocardial ischemia in patients with multivessel coronary disease (MVD). MPI is based on the concept of relative flow reserve. The ability of these techniques to determine the significance of a particular stenosis in the setting of MVD is questionable. Fractional flow reserve (FFR) can determine the significance of individual stenoses. Thirty-six patients with disease involving 88 arteries underwent angiography, FFR, and MPI. FFR was performed using a pressure wire with hyperemia from intracoronary adenosine. Myocardial perfusion images were analyzed quantitatively and segments assigned to a specific coronary artery. The relation between FFR and perfusion was determined for each vascular zone. Of the 88 vessels, the artery was occluded (n=20) or had an abnormal FFR<or=0.75 (n=34) in 54 of 88 (61%). MPI showed no defect in 51 zones (58%). Concordance between angiography, FFR, and MPI was seen in 61 of 88 zones (69%). Discordance was seen in the remaining 27 zones (31%) and was predominantly from the finding of a FFR<0.75 or total occlusion despite no defect on MPI. In conclusion, many patients with MVD show no perfusion defect in zones supplied by arteries with total occlusion or a FFR<0.75. Thus, MPI underestimates ischemic burden and FFR may be better at guiding revascularization decisions than perfusion imaging in patients with MVD.