The enzymic stages of mammalian mitochondrial β-oxidation were elucidated some 30–40 years ago. However, the discovery of a membrane-associated multifunctional enzyme of β-oxidation, a membrane-associated acyl-CoA dehydrogenase and characterization of the carnitine palmitoyl transferase system at the protein and at the genetic level has demonstrated that the enzymes of the system itself are incompletely understood. Deficiencies of many of the enzymes have been recognized as important causes of disease. In addition, the study of these disorders has led to a greater understanding of the molecular mechanism of β-oxidation and the import, processing and assembly of the β-oxidation enzymes within the mitochondrion. The tissue-specific regulation, intramitochondrial control and supramolecular organization of the pathway is becoming better understood as sensitive analytical and molecular techniques are applied. This review aims to cover enzymological and organizational aspects of mitochondrial β-oxidation together with the biochemical aspects of inherited disorders of β-oxidation and the intrinsic control of β-oxidation.