Background: At a population level, inflammatory markers have been shown to predict outcome and response to therapy in patients with atherosclerotic cardiovascular disease. However, current markers are not sufficiently sensitive or specific to provide clinical utility for managing individual patients. We hypothesize that measurement of multiple circulating disease-related inflammatory factors will be more informative, allowing the early identification of vascular wall disease activity. Methods and results: We have investigated whether protein microarray-based abundance measurements of circulating proteins can predict severity of atherosclerotic disease. Using a longitudinal experimental design with apoE-deficient mice and control C57Bl/6J and C3H/HeJ wild-type mice, we measured the time-related serum protein expression of thirty inflammatory markers using a protein microarray. We were able to identify a subset of proteins that classify and predict severity of atherosclerotic disease with high level of accuracy. The timespecific vascular expression of these markers was verified by showing their gene expression in the mouse aorta correlated closely to the temporal pattern of serum protein levels. Conclusions: These data suggest quantification of multiple disease-related inflammatory proteins will provide a more sensitive and specific methodology for assessing atherosclerotic disease activity in humans, and identify candidate biomarkers for such studies.