Abstract Background Fractional flow reserve (FFR) and instantaneous wave-free ratio (iFR) disagree on the hemodynamic significance of a coronary lesion in≈20% of cases. It is unclear whether the physiological pattern of disease is an influencing factor for this. This study assessed whether the physiological pattern of coronary artery disease (CAD) as assessed by angiography derived pullback pressure gradient index (PPGI) influences discordance between FFR and iFR measurement. Methods and results This study is a centralized off-line analysis by an independent academic core laboratory (CORRIB Core lab) of a prospective cohort of 444 vessels with both pressure wire-instantaneous wave free ratio (PW-iFR) and pressure wire-fractional flow reserve (PW-FFR) measurements. The study population consisted of a patients presenting with chronic coronary syndrome and having at least one epicardial coronary artery lesion with a 40% to 90% diameter stenosis by visual assessment on invasive coronary angiography. Three-hundred and ninety vessels (355 patients; mean age, 68±10 years; 70% men) with combined FFR, iFR, QFR and angiography derived PPGI were included. QFR was calculated using the QAngio XA 3D 2.1 software package (Medis Medical Imaging System BV, Leiden, The Netherlands). PPGI was calculated using the QFR 2.1.38.2 Research Edition software package. Cut points for hemodynamic significance were FFR ≤0.80 and iFR ≤0.89, respectively. Vessels were classified into FFR+/iFR+ (n=103; 26.4%), FFR-/iFR+ (n=27; 6.9%), FFR+/iFR- (n=38; 9.7%), and FFR-/iFR- (n=222; 57%) groups.. Median FFR, iFR, and QFR were 0.84 (0.77-0.90), 0.92 (0.88-0.97), and 0.83 (0.73-0.90) respectively. FFR disagreed with iFR in 16.7% (65 of 390). The Median PPGI was 0.75 (0.67-0.85). Vessels with PPGI ≥0.75 was considered to have predominantly focal disease pattern and vessels with PPGI <0.75 was considered to have predominantly diffuse disease pattern. The physiological pattern of disease was classified according to the angiography derived pullback pressure gradient index (PPGI) as predominantly physiologically focal (n=209; 53.6%) or predominantly physiologically diffuse (n=181; 46.4%). The median PPGI was significantly lower in FFR-/iFR+ vessels as compared to FFR+/iFR- vessels [0.65(0.60-0.69) vs 0.82(0.75-0.85), p<0.001). The physiological pattern of disease was the influencing factor relating to FFR/iFR discordance: predominantly physiologically focal was significantly associated with FFR+/iFR- (76.3% [29 of 38]), and predominantly physiologically diffuse was significantly associated with FFR-/iFR+ (96.3% [26 of 27]; P<0.001 for pattern of disease between FFR+/iFR- and FFR-/iFR+ groups). Conclusions The physiological pattern of coronary artery disease was an important influencing factor for FFR/iFR discordance.