Atherosclerosis is a lipid deposition and inflammatory disease that results in considerable morbidity and mortality worldwide. Advances in molecular imaging, particularly near-infrared fluorescence imaging, are now enabling the in vivo study of fundamental biological processes that govern atherogenesis and its complications. Here we describe applications of near-infrared fluorescence reporter technology and intravital fluorescence microscopy to elucidate important biological processes in atherosclerosis in vivo.