Atherosclerosis, a leading cause of morbidity and mortality worldwide, is characterized by the accumulation of lipid deposits inside arterial walls, leading to narrowing of the arterial lumen. A significant challenge in the development of diagnostic and therapeutic strategies is to elucidate the contribution of the various cellular participants, including macrophages, endothelial cells, and smooth muscle cells, in the initiation and progression of the atheroma. This protocol details a strategy using quantum dot nanocrystals to monitor homing and distribution of cell populations within atherosclerotic lesions with high signal to noise ratios over prolonged periods of analysis. This fluorescence-based approach enables the loading of quantum dots into cells such as macrophages without perturbing native cell functions in vivo, and has been used for the multiplexed imaging of quantum dot-labeled cells with biomarkers of atherosclerotic disease using conventional immunofluorescence techniques.