Dietary oils containing large amounts of conjugated linolenic acids (CLnA) may be regarded as a source of conjugated linoleic acids (CLA), which have been suspected to bear health-promoting properties. Indeed, CLnA can be converted into CLA in mammals. The objective of the present study was to investigate the uptake of CLnA and their metabolism into CLA in Caco-2 cells, as a validated in vitro model of the intestinal barrier. Caco-2 cells were incubated for 24 h in the presence of either α-eleostearic, β-eleostearic, catalpic or punicic acid. We first observed that Caco-2 cells take these CLnA up at different rates and then convert them but with varying efficiency depending on the structure of the Δ13 double bond. Finally, the distribution of CLnA between neutral lipids (NL) and phospholipids appeared to be linked to their number of trans double bonds: the higher the number, the higher the accumulation in the NL fraction.