Mitochondrial dysfunction biomarkers are specific indicators used to assess the health and functionality of mitochondria, the cell’s energy-producing organelles. These biomarkers are critical for diagnosing and understanding various diseases linked to impaired mitochondrial function. They include multiple molecules and parameters, such as decreased levels of adenosine triphosphate (ATP), increased production of reactive oxygen species (ROS), and elevated levels of mitochondrial DNA (mtDNA) mutations. Other biomarkers involve changes in gene expression related to mitochondria function, alterations in the structure and number of mitochondria, and the presence of certain enzymes or proteins that indicate mitochondrial stress or damage. These biomarkers are especially relevant in the study of neurodegenerative diseases, mental health disorders, metabolic disorders, aging, and certain cardiovascular and muscular diseases. By measuring these biomarkers, researchers and clinicians can gain insights into the extent of mitochondrial dysfunction, contributing to more accurate diagnoses, monitoring of disease progression, and the development of targeted treatments.