Mitochondria and peroxisomes are organelles that are the primary sites of oxygen usage in eukaryotic cells. Mitochondria carry out cellular respiration—the process that converts energy from food into ATP—the primary form of energy used by cells. Peroxisomes carry out a variety of functions, primarily breaking down different substances such as fatty acids.

Peroxisomes contain up to 50 enzymes and are surrounded by a single membrane. They carry out oxidative reactions that break down molecules and produce hydrogen peroxide (H₂O₂) as a by-product. H₂O₂ is toxic to cells, but the peroxisome contains an enzyme—catalase—that converts H₂O₂ into harmless water and oxygen. In addition, catalase uses H₂O₂ to break down alcohol in the liver into aldehyde and water. However, since H₂O₂ is produced in very low quantities in the body, other enzymes primarily degrade alcohol.

A critical function of the peroxisome is to break down fatty acids in a process called β oxidation. The resulting product—acetyl-CoA—is released into the cytosol and can travel to the mitochondria, where it is used to produce ATP. In mammalian cells, the mitochondria also carry out β oxidation, as well as using products from the catabolism of other energy sources, such as glucose, to produce ATP.

Mitochondria are surrounded by a double membrane: a smooth outer membrane, and an inner membrane that has many folds called cristae. Within the inner membrane is a region called the matrix. During cellular respiration, pyruvate from the breakdown of glucose in the cytoplasm travels into the matrix, where it enters the citric acid cycle. Then, oxidative phosphorylation through the electron transport chain occurs in the inner membrane of the mitochondria, resulting in the production of a significant amount of ATP. The cristae increase the surface area of the inner membrane, providing more regions for ATP production.

Both peroxisomes and mitochondria are self-replicating, but mitochondria additionally have their DNA and ribosomes, enabling them to produce their proteins. Mitochondria and peroxisomes are both highly concentrated in cells where they are needed the most. For example, liver cells—which break down toxic substances in the blood—have high numbers of peroxisomes, and muscle cells—which have large energy requirements—are rich in mitochondria.