Heating polyunsaturated fatty acids (PUFA) produces oxidation products, such as hydroperoxides, aldehydes, and oxypolymers, which could be responsible at least in part for modification of PUFA rumen biohydrogenation (BH). Three in vitro experiments were conducted to investigate the effects of linoleic acid (cis-9,cis-12-C18:2) oxidation products on BH. In the first experiment, we studied the effects of free linoleic acid (FLA), heated FLA (HFLA, at 150 °C for 6h), triacylglycerols of linoleic acid (TGLA), heated TGLA (HTGLA, at 150 °C for 6h), 13-hydroperoxide (13HPOD), trans-2-decenal (T2D), and hexanal (HEX) on BH in vitro after 6 and 24h of incubation. In the second experiment, aldehydes differing in chain length and degree of unsaturation [pentanal, HEX, heptanal, nonanal, T2D, trans-2,trans-4-decadienal (T2T4D)] were incubated in vitro for 5h in rumen fluid. In the third experiment, 9-hydroperoxide (9HPOD), 13HPOD, HEX, or T2T4D were incubated for 1h in rumen fluid inactivated with chloramphenicol to investigate their effects on enzyme activity. In experiment 1, heat treatment of TGLA generated TGLA oxypolymers, did not affect cis-9,cis-12-C18:2 disappearance, but did decrease BH intermediates, especially trans-11 isomers. Heating FLA decreased cis-9,cis-12-C18:2 disappearance and cis-9,trans-11-CLA and trans-11-C18:1 production. Treatment with HEX and T2D did not affect cis-9,cis-12-C18:2 disappearance and barely affected production of BH intermediates. The bacterial community was affected by 13HPOD compared with FLA and HFLA, in parallel with an increase in trans-10 isomer production after a 6-h incubation. After 24h of incubation, 13HPOD decreased trans-11 isomer production, but to a lesser extent than HFLA. In experiment 2, some weak but significant effects were observed on BH, unrelated to chain length or degree of unsaturation of aldehydes; the bacterial community was not affected. In experiment 3, 9HPOD inhibited Δ(9)-isomerization, and both 9HPOD and 13HPOD inhibited Δ(12)-isomerization. We concluded that oxypolymers did not affect cis-9,cis-12-C18:2 disappearance. Heating both esterified and free cis-9,cis-12-C18:2 greatly altered Δ(12)-isomerization. Aldehydes had few effects. Hydroperoxides are responsible, at least in part, for the effects of fat heating: 13HPOD increased trans-10 isomer production (probably by affecting the bacterial community) and decreased trans-11 isomer production by inhibiting Δ(12)-isomerase activity, whereas 9HPOD inhibited both isomerases.