There are increasing needs to develop imaging techniques to study in vivo vascular morphology and function in various mouse models of atherosclerosis. Using ultrasound biomicroscopy (UBM), we developed and validated a new imaging protocol to follow lesion progression in atherosclerotic mice. ApoE and LDL receptor double knockout mice (DKO) with various degree of atherosclerosis and normal control mice were imaged at the level of the ascending aorta using UBM. Average plaque thickness, as well as plaque area were delineated in the short-axis images, and were subsequently compared with histological measurements. We showed that plaque area at this vascular site was closely correlated to total plaque burden from en face measurement ( p < 0.0001). UBM-measured plaque thickness and area correlated with indices for histology measures from the same vascular region ( p < 0.0001 respective p < 0.0001). Furthermore, in 16 DKO mice aged from 32 to 35 weeks, UBM showed significantly weekly increases of IMT in the ascending aorta from 0.106 ± 0.108 mm at 32 weeks of age to 0.256 ± 0.345 mm at 35 weeks of age ( p = 0.0002). In conclusion, this novel imaging protocol provides us with a non-invasive, accurate and inexpensive way to follow lesion progression in mice in vivo.