BACKGROUND AND OBJECTIVES: We report in vivo magnetic resonance imaging (MRI) characteristics and histopathology correlation of the thrombus formation in atherosclerosis the rabbit animal model. DESIGN AND METHODS: Atherosclerosis was induced in white male rabbits with vegetable ghee followed oxidized diet. Baseline MRI of atherosclerosis-recruited rabbits was done and later animals were used for atheroma histopathology characterization. Contiguous cross-sectional T2-weighted fast spin echo MRI images were compared by coronary histopathology. In all animals, coronary aortic wall thickening and atheroma size was measured using MRI. RESULTS: MRI images and digitized histological sections confirmed intraluminal thrombus in 6 (67%) of the 9 animals. MRI data showed correlation with the histopathology for aortic wall thickness (R2 = 0.82, P < 0.0001), lumen area (R2 = 0.88, P < 0.0001) and plaque size (R2 = 0.77, P < 0.0001). Optimized TE and TR parameters and multicontrast enhancement generated better MRI visibility of vulnerable plaque components. The MRI data evaluated % stenosis, plaque burden. Frequency of plaques, plaque height in aorta and coronary artery atheroma was also assessed by histology. In vivo, MRI determined the presence and size of the thrombus in this animal model of atherosclerosis and histopathology defined the plaque disruption. CONCLUSION: The combination of in vivo MRI and comparison with histopathology images of rabbit coronary thrombus may be a research tool for understanding of the pathogenesis of acute coronary plaques.