Mitochondria play a key role in maintaining life by producing ATP and heat. Recent researches have demonstrated that degenerative diseases such as heart failure, obesity/diabetes, cardiovascular disease, and psychiatric diseases are accompanied by mitochondria dysfunction. In this sense, mitochondria medicine considers the significance of mitochondria in human pathology and tries to explain degenerative diseases as a fatal consequence of mitochondria dysfunction. Here, I introduce the fundamentals of mitochondria physiology and present examples showing the relationship between mitochondria dysfunction and chronic complex diseases. Although mitochondria medicine uses a molecular biological approach predominantly, a biomedical engineering approach might play a critical role in unveiling the complexity of mitochondria medicine and in its application to the diagnosis and treatment of chronic diseases. Thus, I also briefly review the prospects of research using biomedical engineering methods.