A variety of human diseases, including neurodegenerative disorders, ischemic heart disease, diabetes, and cancer have been reported to be associated with mitochondrial dysfunction. Because of this, mitochondrial therapy is expected to be useful and productive in the treatment of such diseases. We previously reported on the development of a MITO-Porter, a liposome-based nanocarrier that permits macromolecular cargos to be delivered into mitochondria via membrane fusion. Intracellular observations using the green fluorescence protein as a model macromolecule provided confirmation that a macromolecule could be delivered to mitochondria in living cells by the MITO-Porter. Here, we present our current findings on the development of mitochondrial medicine and mitochondrial gene therapy based on our mitochondrial drug delivery system (DDS). In this review, we propose “mitochondrial DDS” as a theme for “DDS research for innovative drug development” and discuss the contribution of mitochondrial DDS to innovative drug development.