The effects of three emulsifying methods on ruminal fatty acid biohydrogenation (BH) in vitro were compared. Using a static in-vitro gas test system, four replicates of each treatment were incubated in buffered ruminal fluid. Hemicellulose (300 mg dry matter) was supplemented either with or without linoleic acid (9c12c-18:2, 5% in diet dry matter) and incubated for 4 and 24 h. Three methods of emulsifying 9c12c-18:2 were tested: (1) ethanol, (2) Tween 80, and (3) sonication. The products were then compared to non-emulsified 9c12c-18:2. Out of the three emulsifying methods tested, ethanol and sonication resulted in stable 9c12c-18:2 emulsions, indicating good 9c12c-18:2 distribution, while the Tween 80 emulsion was less stable. BH was strongly inhibited by treating 9c12c-18:2 with ethanol and sonication at different steps of the BH-pathway, resulting in changed concentrations of certain BH intermediates. The fatty acid profile generated from the major BH-pathways of 9c12c-18:2 with Tween 80 was comparable to that without emulsification after 24 h of incubation. We conclude that it is not recommended to emulsify lipids before incubating them in vitro when investigating fatty acid BH. If emulsification of 9c12c-18:2 is necessary, Tween 80 seems to be the method that interferes least with BH.