Atherosclerosis is a growing health challenge globally, and despite our knowledge of the disease has increased over the last couple of decades, many unanswered questions remain. As molecular imaging can be used to visualize, characterize and measure biological processes at the molecular and cellular levels in living systems, this technology represents an opportunity to investigate some of these questions in vivo. In addition, molecular imaging may be translated into clinical use and eventually pave the way for more personalized treatment regimes in patients. Here, we review the current knowledge obtained from in vivo positron emission tomography studies of atherosclerosis performed in small animals.