Virtual Histology (VH) intravascular ultrasound (IVUS) allows differentiation between 4 different tissue phenotypes. However, the current classification tree for analysis cannot differentiate the presence of intramural thrombus. The aim of this study was to evaluate the impact of intramural thrombus for correlative accuracy between in vitro histopathology of coronary atherosclerotic plaque obtained by directional coronary atherectomy and corresponding in vivo tissue characterization obtained by VH IVUS. Coronary IVUS imaging of 30 coronary artery lesions was obtained using a 20-MHz phased-array IVUS catheter with a motorized pull-back system at set 0.5 mm/s. The debulking region of the in vivo histologic image was predicted from comparison between pre- and post-first debulking VH IVUS images. Cross-sectional histologic slices were cut every 0.5 mm starting from the most proximal part of the formalin-fixed debulking tissue. Histologic slices were divided into 2 groups by the presence or absence of pathologic thrombus. A total of 259 in vitro histologic slices were obtained, and pathologic thrombus was detected in 81 slices. Correlation was favorable, with high sensitivity for all plaque components, but specificities for fibrous (thrombus slices vs nonthrombus slices 36% vs 94%) and fibrofatty (9% vs 60%) tissue were lower in thrombus slices. Therefore, predictive accuracies for the 2 plaque components were lower in thrombus slices (fibrous tissue 78% vs 99%, fibrofatty tissue 68% vs 83%, respectively). In conclusion, intramural thrombus was colored as fibrous or fibrofatty by VH IVUS, reducing VH accuracy in these kinds of lesions.