Gene therapy for ischemic diseases has been developed with various growth factors and anti-apoptotic genes. However, non-specific expression of therapeutic genes may induce deleterious side effects such as tumor formation. Hypoxia-specific regulatory systems can be used to regulate transgene expression in hypoxic tissues, in which gene expression is induced in ischemic tissues, but reduced in normal tissues by transcriptional, translational or post-translational regulation. Since hypoxia-inducible factor 1 (HIF-1) activates transcription of genes in hypoxic tissues, it can play an important role in the prevention of myocardial and cerebral ischemia. Hypoxia-specific promoters including HIF-1 binding sites have been used for transcriptional regulation of therapeutic genes. Also, hypoxia-specific untranslated regions (UTRs) and oxygen dependent degradation (ODD) domains have been investigated for translational and post-translational regulations, respectively. Hypoxia-specific gene expression systems have been applied to various ischemic disease models, including ischemic myocardium, stroke, and injured spinal cord. This review examines the current status and future challenges of hypoxia-specific systems for safe and effective gene therapy of ischemic diseases.