Trihydroxycoprostanoyl-CoA oxidase and pristanoyl-CoA oxidase, purified from rat liver, both catalyse the desaturation of 2-methyl-branched acyl-CoAs. Upon incubation with the pure isomers of 2-methylpentadecanoyl-CoA, both enzymes acted only on the S-isomer. The R-isomer inhibited trihydroxycoprostanoyl-CoA oxidase but did not affect pristanoyl-CoA oxidase. The activity of both enzymes was suppressed by 3-methylheptadecanoyl-CoA. Valproyl-CoA and 2-ethylhexanoyl-CoA, however, did not influence the oxidases. Although only one isomer of 25R,S-trihydroxycoprostanovl-CoA was desaturated by trihydroxycoprostanoyl-CoA oxidase, isolated peroxisomes were able to act on both isomers, suggesting the presence of a racemase in these organelles. Given the opposite stereoselectivity of the 26-cholesterol hydroxylase and of the oxidase, the racemase is essential for bile acid formation.