In vivo, cardiac-gated, black-blood, and ex vivo magnetic resonance microscopy (MRM) images of the aortic root, and histopathology data were obtained from 12 transgenic and wildtype (WT) mice. MRM was performed using a black-blood imaging spin-echo sequence with upstream and downstream inflow saturation pulses to obtain aortic root images in three contrast techniques: proton density-weighted (PDW), T 1 -(T 1 W), and T 2 -weighted (T 2 W). Aortic wall thickness and area were measured and correlated with histopathology data (R > 0.90). Ex vivo lesion components (lipid core, fibrous tissue, and cell tissue) were identified and characterized by differing image contrast in PDW, T 1 W, and T 2 W MRM, and by histopathology. The differences between WT and transgenic mice for maximal wall thickness and area were statistically significant (P < 0.05). This study demonstrates the feasibility of in vivo murine aortic root lesion assessment and ex vivo plaque characterization by MRM. Magn Reson Med 49:381-385, 2003.