Manipulation of rumen biohydrogenation (BH) is of great importance, since decreased BH of linolenic acid (LNA) and linoleic acid (LA) is linked to increased content of the beneficial polyunsaturated fatty acids (PUFA) in dairy products and decreased content of trans fatty acids (FAs). We hypothesized that PUFA esterified to the complex lipid fractions are less prone to BH compared with PUFA esterified to the simple lipid fractions due to reduced lipolysis. In vitro rumen BH of different single lipid fractions was investigated, including free fatty acids (FFA), and esterified FA to triglycerides (TG), cholesterol esters (CE), and phospholipids (PL). A mixture of a buffer solution and rumen fluid was incubated with different lipid fractions, and C18 FAs were quantified by gas chromatography. In vitro BH kinetic parameters were quantified according to Michaelis–Menten equation and the maximum BH (Vmax) and time to achieve 50% of maximum amount (KM) estimated. Regardless of fatty acids, BH in CE and PL was lower than FFA and TG. The highest amount of cis‐9, trans‐11 conjugated linoleic acid (CLA) and trans‐10, cis‐12 CLA was observed in lipid fractions containing LA and LNA, respectively, regardless of lipid fractions. The present study demonstrates the importance of lipid fractions on BH of LNA and LA and formation of CLA isomers. The results show that BH of FAs depends on the lipid fractions.