Background Brain microvessels (MVs) may represent a more vulnerable segment of the cerebral circulation than large arteries during aging, diabetes, and/or minor strokes. Adverse changes in MVs have been implicated in the development of cognitive impairment, vascular dementia, and Alzheimer's disease. However, development of effective therapies has been hampered by lack of understanding of the underlying mechanisms that negatively affect MVs compared to large arteries. The purpose of this study was to identify potential mechanisms underlying the vulnerability of MVs compared to large arteries to aging and pathological conditions and the impact of sex using quantitative RNA sequencing (RNAseq). Methods Cerebral arteries (anterior and middle cerebral, basilar, circle of Willis) and cortical MVs (end arterioles, capillaries, venules) were isolated from young age-matched male and female C57BL6J mice. Arteries and MVs were then used for 3 vs. 3 quantitative RNAseq. RNASeq analyses were performed using the Illumina NextSeq 550 sequencing system. RNASeq expression analysis was performed using Kallisto (v0.46.0), and Sleuth (v0.30.0) with the mouse transcriptome index. Results For females, the RNAseq analysis identified 14,325 genes out of 51,661genes examined with significant (p < 0.05) differences between arteries and cortical MVs. The greatest differences (3 to 6 times) were seen in the expression of the following genes: Thrombospondin-2 (calcium ion binding, negative regulation of angiogenesis), SPARC-related modular calcium-binding gene 1, Megakaryocyte-associated tyrosine protein-kinase (ATP binding), Prostaglandin-H2 D-isomerase (fatty acid synthesis), Solute carrier family 7 member 2, SOGA family member 3, Gelsolin (aging and apoptotic process), potassium voltage-gated channel subunits, and glutamate receptor subunits (Gria, Grin). While most of the Gria, Grin and potassium channels genes were abundantly expressed in MVs, thrombospondins, prostaglandins and apoptosis-related genes were more highly expressed in large arteries. The RNAseq profiles comparing arteries to MVs for males were very different than for females (extracellular matrix binding, regulation of smooth muscle contraction and growth factors, mostly). Conclusion We found substantial differences in the gene expression of brain large arteries and cortical MVs in mice and these differences may account for increased vulnerability of smaller blood vessels to aging and stress. For example, increased expression of glutamatergic receptors in MVs might be associated with enhanced vulnerability to damage and dysfunction of this segment of the cerebral circulation due to stress. The finding that RNAseq profiles comparing large arteries and cortical MVs differ between males and females may provide the basis for sex-dependent differences in the vulnerability and severity of neurological disorders in humans.