Aging is a multifactorial process during which physiological alterations occur in all tissues. A decline in mitochondrial function plays an important role in the process of aging and in aging-associated diseases. The mitochondrial genome encodes 13 essential subunits of protein complexes belonging to the oxidative phosphorylation system, while most of the mitochondria-related genes are encoded by the nuclear genome. Coordination between the nucleus and mitochondria is crucial for the regulation of mitochondrial biogenesis and function. In this review, we will discuss aging-related mitochondrial dysfunction in various tissues and its implication in aging-related diseases and the aging process.