Although forage lipid is generally rich in polyunsaturated fatty acids (PUFA), recovery of these fatty acids (FA) in milk and meat of ruminant origin is generally low, due to microbial biohydrogenation (BH) taking place in the rumen. Since lipolysis is a prerequisite for BH, the latter process is expected to be enhanced when (conserved) forages contain lower levels of esterified FA (particularly polar lipids; PL). However, this was not observed in former studies with red clover (Trifolium pratense L.). Furthermore, red clover inclusion in the herbivore's diet was associated with decreased rumen BH as compared with other forages. Differences in plant lipase activity during wilting and ensiling has been attributed to changes in disappearance from the PL fraction, but a potential role of microbial lipases in silo has not yet been elucidated. Therefore, the aims of the present study were to assess whether BH of red clover FA is linked with PL levels of the (conserved) starting material and to clarify the possible role of in silo microbial activity on PL disappearance. In order to obtain sufficient variation in forage PL and microbial activity, laboratory-scale silages were made by wilting and ensiling damaged or undamaged red clover using molasses or formic acid as ensiling additive, while perennial ryegrass (Lolium perenne L.) was used as a control. Distribution of lipids within three lipid fractions (PL, free FA and neutral lipids) in forages was determined and BH calculated after 24 h in vitro rumen incubation. Results indicated microbial lipases in silages did not enhance FA disappearance from the PL fraction. A gradual decrease of FA in the PL fraction upon conservation was found, both in red clover and ryegrass, irrespective of the degree of damage. In red clover PL losses started from the wilting phase, while substantial PL disappearance from ryegrass only started upon ensiling. Proportions of PUFA remaining in the PL fraction after wilting and ensiling of red clover were positively correlated with PUFA BH, while this effect was not observed for ryegrass. Red clover PUFA seemed to be partially protected against ruminal BH, while disappearance of FA from the PL fraction did not seem to be hampered. Results indicated the encapsulation mechanism as a consequence of protein-bound phenol formation induced by polyphenol oxidase is still the most probable hypothesis to explain red clover's increased flow of PUFA across the rumen