Exploration of molecular mechanisms involved in alterations of cerebral blood vessels in pathology such as chronic kidney disease implies cerebral vessel isolation for proteins and mRNAs quantification. We describe an updated method to isolate brain microvessels from wild type (WT) mice at 14 weeks of age. The quality of cerebral arterioles preparation was determined by measuring the enzymatic activity of gamma-glutamyl transpeptidase, an enzyme that is especially expressed in cerebral microvessels, and the quantitative expression (Western Blot) of platelet endothelial cell adhesion molecule-1 (PECAM-1), alpha-actin and gamma-enolase as markers of respectively endothelial cells, smooth muscle cells and neurons. We then assessed PECAM-1 expression in 14 and 20 weeks old ApoE(-/-) and WT mice. PECAM-1 expression was increased in 14 weeks old ApoE(-/-) mice compared to age matched WT mice. This difference in PECAM-1 expression disappeared at 20 weeks of age. These findings indicate that the present method of mice cerebral arterioles isolation is a valid method. Moreover, PECAM-1 expression, a marker of endothelial cells, changes with age in cerebral arterioles of ApoE(-/-) mice.