Non-invasive diagnosis of coronary artery disease (CAD) is achieved using rest and stress myocardial perfusion imaging (MPI) techniques. Currently, the MPI technique that is a standard of care is the Single Photon Emission Computed Tomography (SPECT). However, comparatively accurate and reliable MPI diagnostic test known as Positron Emission Tomography (PET) is also available and gaining increasing popularity. In this study, a comparison is made between the impairments and left ventricular (LV) ejection fraction (EF) reported by SPECT and PET. In addition, using PET data, flow defects were quantified using coronary flow reserve (CFR: ratio of flow at stress to the rest) in four coronary territories, left ventricle (LV), left circumflex (LCX), right coronary artery (RCA) and left anterior descending (LAD). Three patients with previous SPECT and suspected CAD were consented and further assessed with a PET cardiac N-13 ammonia scan according to the study protocol. The comparisons of the two imaging modalities showed discordance for patients 1 and 2 while they concurred for the patient 3. More importantly, quantification of the extent of defect showed an abnormal CFR value (< 2) of 1.67 (LCX) and 1.57 (RCA) for the patient 1 and 1.67 (LAD) and 1.75 (RCA) for patient 2. For the third patient, CFR value was abnormal at 0.85 for the RCA. Therefore, in contrast to SPECT, quantification of flow impairment using PET MPI in individual coronary territories will aid in better diagnosis of CAD.