Structural proteins such as elastin and collagen can be readily imaged by using two-photon excitation and second-harmonic generation microscopic techniques, respectively, without physical or biochemical processing of the tissues. This time- and effort-saving advantage makes these imaging techniques convenient for determining the structural characteristics of blood vessels in vivo. Fibrillar collagen is a well-known element involved in the formation of atherosclerotic lesions. It is also an important component of the fibrous cap responsible for structural stability of atherosclerotic plaques. High resolution in vivo microscopic imaging and characterization of atherosclerotic lesions in animal models can be particularly useful for drug discovery. However, it is hindered by the limitations of regular microscope objectives to gain access of the tissues of interest and motional artifacts. We report a technique that facilitates in vivo microscopic imaging of carotid arteries of rodents using conventional microscope objectives, and at the same time avoids motional artifacts. As a result, collagen, elastin, leukocytes, cell nuclei, and neutral lipids can be visualized in three dimensions in live animals. We present and discuss in vivo imaging results using a flow cessation mouse model of accelerated atherosclerosis.