Objective: To compare the gene expression profiles of the aorta specimens between patients with Stanford type B aortic dissection (AD) and controls. Materials and Methods: Samples of descending aorta were collected from patients with type B AD (n = 12) and from multiorgan donors as controls (n = 12). Phalanx whole genome microarray was used to analyze differential gene expression. Results: Of the 6375 probes validated, 623 genes were found to be differentially expressed between patients with type B AD and controls (fold change ≥2). Gene ontology analysis identified significantly enriched gene groups pertaining to cell–cell adhesion, extracellular matrix, cell–matrix adhesion, cytoskeleton, immune and inflammatory response, and apoptosis. Conclusion: Genes encoding components related to integrity and strength of the aortic wall were downregulated, whereas those related to inflammatory response were upregulated in type B AD. The altered patterns of gene expression indicate preexisting structural defects that are probably a consequence of insufficient remodeling of the aortic wall.