Peroxisomal beta-oxidation is involved in the degradation of different fatty acids or fatty acid derivatives including eicosanoids (prostaglandins, leukotrienes, thromboxanes), dicarboxylic fatty acids, very long-chain fatty acids, pristanic acid, bile acid intermediates (di- and trihydroxycoprostanoic acids), and xenobiotics. Separate beta-oxidation systems are probably active inside peroxisomes, each acting on a distinct set of substrates, as suggested by the discovery of multiple acyl-CoA oxidases. Using specific substrates or selective conditions, we can distinguish in rat liver the action of acyl-CoA oxidases (type I and II), a pristanoyl-CoA oxidase and a trihydroxycoprostanoyl-CoA oxidase and, in human liver, of acyl-CoA oxidase (type I and Il) and a branched-chain acyl-CoA oxidase. When incubated with suitable CoA-esters, these different oxidases can be measured in a similar fashion by following fluorimetrically the dimerization of homovanillic ai:id, catalysed by peroxidase in the presence of hydrogen peroxide. The optimal assay conditions and possible pitfalls in this type of coupled assay are discussed. This knowledge can be used to reveal the existence of peroxisomal disorders in which only one acyl-CoA oxidase is deficient.