Cerebral aneurysms are a major cause of subarachnoid hemorrhage, but the mechanism of their development remains unclear. In this study, we investigated candidate genes whose expression is significantly changed during the development of experimentally induced cerebral aneurysms using adaptor-tagged competitive polymerase chain reaction (ATAC-PCR). Twenty-four rats received sham operation (control) or the operation for the induction of experimental cerebral aneurysms. Rats were sacrificed at time 0, 2 weeks, 1 month and 3 months after the operation (n = 6 for each group). RNAs from right anterior cerebral artery/olfactory artery (ACA/OA) bifurcations were assessed via a 191-gene data matrix expression profile by ATAC-PCR. We identified 15 genes whose expression is significantly altered during cerebral aneurysm formation, including major heparan sulfate proteoglycan, cathepsin B, hevin and β4-integrin. We also confirmed protein expression of β4-integrin in rat cerebral aneurysms by quantitative real-time PCR and immunohistochemistry. The ATAC-PCR revealed temporal changes in gene expression during the development of experimental cerebral aneurysms. The genes that were significantly changed in this study would be the candidates for future studies concerning the development of cerebral aneurysms.