High-density microarrays were recently used to identify the genomic profiles of vascular cells during atherogenesis. This strategy succeeded in identifying both biomarkers and underlying biological processes of the pathological development. However, data documenting the early stages of disease are sparse. To identify the mechanisms involved in atherogenesis, we examined differential gene expression in the aorta of C57BL/6J mice fed a high-fat diet (HFD) or a low-fat diet (LFD), for a short period of time of three weeks. The cDNAmicroarray analysis revealed that the expression of 448 genes was significantly different between the two groups. As expected, key genes involved in lipid synthesis or catabolism were down- and upregulated, respectively, representing a normal gene expression response to increased cellular lipid levels. Overrepresented biological processes were identified by Gene Ontology (GO) analysis, which revealed that aortic cells differentiate into a new phenotype in mice fed the HFD. This phenotype was represented by changes in the expression of 81 genes associated with extracellular matrix and cytoskeletal modifications. Some of these genes were previously shown to be involved in the cardiovascular diseases process. In conclusion, short-term HFD consumption results in metabolic disturbances leading to a broad induction of genes involved in vessel architecture remodelling.