Macrophage foam cells are critical mediators in atherosclerosis plaque development. A better understanding of the in vivo transcript profile of foam cells during the formation and progression of lesions may lead to novel therapeutic interventions. Toward this goal, we demonstrate for the first time that foam cell-specific RNA can be purified from atherosclerotic arteries, a tissue of mixed cellular composition. Foam cells from apolipoprotein (apo) E-^/- mice were isolated by laser capture microdissection (LCM); RNA was extracted and used for molecular analysis by real-time quantitative polymerase chain reaction. Compared to whole tissue, a significant enrichment of foam cell-specific RNA transcripts was achieved. Furthermore, to test the ability to quantify differences in gene expression in response to an inflammatory stimulus, apoE-/- mice were injected with lipopolysaccharide, after which the transcriptional induction of the inflammatory mediators, VCAM, ICAM, and MCP-1, was observed in lesional macrophage foam cell RNA. These approaches will facilitate the study of macrophage gene expression under various conditions of plaque formation, regression, and response to genetic and environmental perturbations.