Background-The cells that form the arterial wall contribute to multiple vascular diseases. The extent of cellular heterogeneity within these populations has not been fully characterized. Recent advances in single cell RNA-sequencing makes it possible to identify and characterize cellular subpopulations.Methods-We validate a method for generating a droplet-based single cell atlas of gene expression in a normal blood vessel. Enzymatic dissociation of four whole mouse aortas was followed by single cell sequencing of over 10,000 cells.Results-Clustering analysis of gene expression from aortic cells identified 10 populations of cells representing each of the main arterial cell types-fibroblasts, vascular smooth muscle cells (VSMCs), endothelial cells (ECs), and immune cells including monocytes, macrophages, and lymphocytes. The most significant cellular heterogeneity was seen in the 3 distinct EC populations. Gene set enrichment analysis of these EC subpopulations identified a lymphatic EC cluster and two other populations more specialized in lipoprotein handling, angiogenesis, and extracellular matrix production. These subpopulations persist and exhibit similar changes in gene expression in response to a Western diet. Immunofluorescence for Vcam1 and Cd36 demonstrates regional heterogeneity in EC populations throughout the aorta.