The mouse has become the de facto model for the majority of atherosclerosis studies. Studies involving the quantification of lesions in mouse models of the disease represent the basis of our evolving concepts on the biochemical and cellular mechanisms underlying the atherogenic process. Many issues of experimental design, including specific model, strain, gender, atherogenic stimulus, duration of study, group size, and statistical analysis may influence the outcome and interpretation of atherosclerosis studies. The selection of vascular bed in which to quantify atherosclerotic lesion size could also impact the interpretation of results. Early studies quantified atherosclerotic lesion size in either specific regions or all of the aortic sinus. Measurement of atherosclerosis throughout the aortic intimal surface has become a common mode for defining lesion size. It is likely that other vascular regions will be increasingly used. In addition to size, there is an increased emphasis on identifying and quantifying the cellular and chemical composition of atherosclerotic lesions.