Objective Differences in microvascular integrity can diversely influence the functional assessment of epicardial coronary artery disease in each patient. We investigated the relevance of the index of microcirculatory resistance (IMR) and fractional flow reserve (FFR) of intermediate coronary lesions. Methods The IMR and FFR were measured in 67 intermediate coronary lesions of the left anterior descending artery of 67 patients, by using a pressure sensor/thermistor-tipped guidewire. Results To assess the differences in FFR in relationship to the IMR value, patients were divided into tertile IMR groups as follows: Low-IMR (n=22, IMR 14±3), Mid-IMR (n=23, IMR 21±2), and High-IMR (n=22, IMR 36±10). An analysis of variance showed that the High-IMR group had significantly higher FFR values (0.87±0.07) than the Low-IMR group (0.81±0.08) (p=0.03). Functionally significant lesions with FFR ! 0.8 accounted for 9% of lesions in the High-IMR group, 36% in the Low-IMR group and 22% in the Mid-IMR group (p=0.02). In the multivariate logistic analysis, the IMR value was an independent determinant of FFR ! 0.8 (p=0.03). Conclusion In patients with a high IMR, intermediate lesions as identified with visual estimation were more frequently functionally insignificant. The IMR can provide additional information in understanding the mismatch between the anatomical and functional severity of intermediate coronary stenosis.