Background: Hypoxia-inducible factor-1 (HIF-1) is a transcription factor that regulates the adaptive response to hypoxia in mammalian cells. It consists of a regulatory subunit HIF-1 alpha, which accumulates under hypoxic conditions, and a constitutively expressed subunit, HIF-1 beta. In this study, we investigated HIF-1 alpha naked DNA-induced angiogenesis in a cerebral ischemic model in vivo. Methods: We utilized a rat encephalo-myo-synangiosis (EMS) model and inoculated HIF-1 alpha DNA into the brain surface or the temporal muscle. We analysed whether HIF-1 alpha induced angiogenic factors and collateral circulation. Results: A histological section treated with HIF-1 alpha DNA showed an increased expression of HIF-1 alpha and VEGF with collateral circulation, in comparison with control DNA (p < 0.01). The HIF-1 alpha transcription factor is able to promote significant angiogenesis development. Conclusion: These results suggest the feasibility of a novel approach for therapeutic collateral circulation of cerebral ischemia in which neovascularization may be achieved indirectly using a transcriptional regulatory strategy.