At the balance between human health and disease (from the very first moments to the end of life), the mitochondrion is central players because of its metabolic role in adenosine triphosphate synthesis, cell signaling, immune response, and other processes of clinical interest. On the other hand, impairments at the optimal mitochondria function have important consequences in complex diseases, such as heart disease, diabetes, and cancer, among others. These mitochondrial impairments can occur at any age damaging multiple body systems, which have prompted the mitochondrial medicine development. Since mitochondrial diseases have great variability in their clinical manifestations, early studies were centered on mitochondriopathies, however nowadays, this focus has broadened to understand and encompass the mitochondrial role of in diseases development of both pediatric and adult age. The mitochondria potential to improve diagnostic, prognostic, and treatment response strategies has been revealed by experimental approaches using proteomics, genomics, and metabolomics to identify clinical biomarkers showing disease development. Thus, the perspective of mitochondria-based medicine recognizes the importance of generating scientific evidence related to mitochondria and their role in pathological conditions from a comprehensive approach.