A variety of diseases including neurodegenerative, neuromuscular diseases, diabetes, obesity and cancer are considered to be caused by mitochondrial dysfunction. Efficient delivery of therapeutic agents to mitochondria is necessary to treat these diseases. In the past decade, mitochondria targeted nanoparticles have been shown to be a promising deliver system. In this review, functionalized nanosystems targeting mitochondria are discussed. More efforts are needed to bring these novel nanosystems from bench top to bed side.