Objectives: The authors sought to evaluate the influence of coronary microcirculatory dysfunction (CMD) on the diagnostic performance of the quantitative flow ratio (QFR). Background: Functional angiographic assessment of coronary stenoses based on fluid dynamics, such as QFR, constitutes an attractive alternative to fractional flow reserve (FFR). However, it is unknown whether CMD affects the reliability of angiography-based functional indices. Methods: FFR and the index of microcirculatory resistance (IMR) were measured in 300 vessels (248 patients) as part of a multicenter international registry. QFR was calculated at a blinded core laboratory. Vessels were classified into 2 groups according to microcirculatory status: low IMR (<23 U), and high IMR (≥23 U, CMD). The impact of CMD on the diagnostic performance of QFR, as well as on incremental value of QFR over quantitative angiography, was assessed using FFR as reference. Results: Percent diameter stenosis (%DS) and FFR were similar in low- and high-IMR groups (%DS 51 ± 12% vs. 53 ± 11%; p = 0.16; FFR 0.80 ± 0.11 vs. 0.81 ± 0.11; p = 0.23, respectively). In the overall cohort, classification agreement (CA) between QFR and FFR and diagnostic efficiency of QFR (area under the receiver-operating characteristics curve [AUC]) were high (CA: 88%; AUC: 0.93 [95% confidence interval (CI): 0.90 to 0.96]). However, when assessed according to microcirculatory status, a significantly lower CA and AUC of QFR were found in the high-IMR group as compared with the low-IMR group (CA: 76% vs. 92%; p < 0.001; AUC: 0.88 [95% CI: 0.79 to 0.94] vs. 0.96 [95% CI: 0.92 to 0.98]; p < 0.05). Compared with angiographic assessment, QFR increased by 0.20 (p < 0.001) and by 0.16 (p < 0.001) the AUC of %DS in low- and high-IMR groups, respectively. Independent predictors of misclassification between QFR and FFR were high IMR and acute coronary syndrome. Conclusions: CMD decreases the diagnostic performance of QFR. However, even in the presence of CMD, QFR remains superior to angiography alone in ascertaining functional stenosis severity.