We evaluated the relationships between coronary flow reserve (CFR) and relative flow reserve (RFR) measured by N-13 ammonia positron emission tomography (PET) for characterization of epicardial coronary artery disease (CAD). Sixty-nine consecutive stable angina patients underwent N-13 ammonia PET, coronary computed tomography angiography (CCTA), and if necessary, invasive coronary angiography (CAG) within 2weeks. Myocardial blood flow (MBF), CFR, RFR, and coronary vascular resistance of the reference arterial territory (CVRref) were measured by N-13 ammonia PET. The presence of significant stenosis (SS) and diffuse atherosclerosis (DA) was evaluated on CCTA and CAG. Functional parameters measured by PET were compared among arteries with and without SS and DA. Arteries with SS and those with DA showed significantly lower stress MBF, as compared to those without. RFR was significantly lower in arteries with SS as compared to those without, while CFR was not. CFR was significantly lower in arteries with DA as compared to those without, while RFR was not. Among arteries without SS, CFR was significantly lower in those with DA as compared to those without. However, among arteries with SS, CFR was similar between those with and without DA. In contrast, RFR was significantly lower in arteries with SS, regardless of the presence of DA. CFR and RFR showed a weak positive correlation (r=0.269) with discordance in 24 cases (35%). Among the arteries with CFR-RFR discordance, the prevalence of DA was significantly higher in those with low CFR but preserved RFR, as compared to those with preserved CFR but low RFR (75 vs 25%, p=0.028). CVRref was significantly higher in arteries with DA, implicating a correlation of DA with underlying microvascular disease. CFR and RFR measured by myocardial perfusion PET could provide a comprehensive information for characterization of epicardial CAD.