Minor aberrant pathways of cholesterol biosynthesis normally produce only trace levels of abnormal sterol metabolites but may assume major importance when an essential biosynthetic step is blocked. Cholesta-5,8-dien-3  -ol, its ⌬ 5,7 isomer, and other noncholesterol sterols accumulate in subjects with the Smith-Lemli-Opitz syndrome (SLOS), a severe developmental disorder caused by a defective ⌬ 7 sterol reductase gene. We have explored the formation and metabolism of unsaturated sterols relevant to SLOS by incubating tritium-labeled ⌬ 5,8 , ⌬ 6,8 , ⌬ 6,8(14) , ⌬ 5,8( 14) , and ⌬ 8 sterols with rat liver preparations. More than 60 different incubations were carried out with washed microsomes or the 10,000 g supernatant under aerobic or anaerobic conditions; some experiments included addition of cofactors, fenpropimorph (a ⌬ 8 -⌬ 7 isomerase inhibitor), and/or AY-9944 (a ⌬ 7 reductase inhibitor). The tritium-labeled metabolites from each incubation were identified by silver ion high performance liquid chromatography on the basis of their coelution with unlabeled authentic standards, as free sterols and/ or acetate derivatives. The ⌬ 5,8 sterol was converted slowly to cholesterol via the ⌬ 5,7 sterol, which also slowly isomerized back to the ⌬ 5,8 sterol. The ⌬ 6,8 sterol was metabolized rapidly to cholesterol by an oxygen-requiring pathway via the ⌬ 7,9(11) , ⌬ 8 , ⌬ 7 , and ⌬ 5,7 sterols as well as by an oxygen-independent route involving initial isomerization to the ⌬ 5,7 sterol. The ⌬ 8 sterol was partially metabolized to ⌬ 5,8 , ⌬ 6,8 , ⌬ 7,9(11) , and ⌬ 5,7,9(11) sterols when isomerization to ⌬ 7 was blocked. The combined results were used to formulate a scheme of normal and aberrant biosynthetic pathways that illuminate the origin and metabolic fate of abnormal sterols observed in SLOS and chondrodysplasia punctata. -Ruan, B., J. Tsai, W. K. Wilson, and G. J. Schroepfer, Jr. Aberrant pathways in the late stages of cholesterol biosynthesis in the rat: origin and metabolic fate of unsaturated sterols relevant to the Smith-Lemli-Opitz syndrome.