Objectives of this study were to compare fatty acid composition of subcutaneous adipose tissue of entire boars, barrows, and male pigs vaccinated against boar taint with a vaccine containing a GnRH analogue-protein conjugate (Improvac, Pfizer Animal Health) and to investigate the association between fatty acid composition and protein expression of key lipogenic enzymes in entire boars, barrows, and vaccinated pigs. Differences between groups were observed in the content of total SFA (P≤0.001), MUFA (P=0.035), and n-6 PUFA (P≤0.001) but not n-3 PUFA (P=0.373). Total SFA were greater (P<0.001) in barrows and vaccinated pigs compared with entire animals. This was accompanied by an increase (P<0.05) in the protein expression of the lipogenic enzyme fatty acid synthase in barrows and vaccinated pigs. Total MUFA content was increased (P<0.001) in barrows compared with entire and vaccinated pigs. This was not accompanied (P>0.05) by an increase in expression of stearoyl-CoA desaturase protein, the enzyme catalyzing MUFA biosyntheses. Total n-6 PUFA content did not differ (P<0.001) between entire and vaccinated pigs but was lower in barrows. Expression of Δ6-desaturase protein, one of the key enzymes of PUFA biosynthesis, was greater (P<0.05) in vaccinated pigs than in barrows but did not differ significantly between vaccinated and entire animals. We conclude that fatty acid profile of animals vaccinated against boar taint is similar to that of entire male pigs and that the effect of physical castration and vaccination on fatty acid composition involves changes in lipogenic enzyme protein expression.