This article summarizes our current knowledge of the metabolic pathways present in mammalian peroxisomes. Emphasis is placed on those aspects that are not covered by other articles in this issue: peroxisomal enzyme content and topology; the peroxisomal beta-oxidation system; substrates of peroxisomal beta-oxidation such as very-long-chain fatty acids, branched fatty acids, dicarboxylic fatty acids, prostaglandins and xenobiotics; the role of peroxisomes in the metabolism of purines, polyamines, amino acids, glyoxylate and reactive oxygen products such as hydrogen peroxide, superoxide anions and epoxides.