A mechanism-based logical approach is a mainstream of current novel drug therapy development in the context of these trends and, therefore, the elucidation of gene function and the molecular level mechanism analysis of diseases at an individual level in mammals are essential in addition to that in cultured cells. In vivo gene transfection techniques are also indispensable for these purposes as well as the evaluation of gene therapy and nucleic acid-based therapy approaches and clinical applications during the process of development of novel drug therapies. Various recombinant virus and synthetic carrier-mediated transfection methods have been reported, however, above all, naked plasmid DNA transfection without virus vectors, synthetic carriers and special physical devices has attracted much attention, because of its advantages including convenience of preparation and handling and lack of toxicity associated with the transfection agents. In this review, I collect the information of these naked plasmid DNA transfection methods involving tissue pressure-mediated transfection from the comprehensive view point including side effects. Additively, the key physiological phenomena affecting transgene expression, especially activation of transcriptional factors, are reviewed. Combined with conventional approach based with biodistribution control, regulation of physiological change in transfected cells will provide spatial- and temporal-controlled transgene expression at various organs, which leads us to elucidate mechanism of diseases and to develop novel drug therapy in near future.