Trans polyunsaturated fatty acids are produced during heat treatment of oils, such as deodorization and frying. The detailed metabolic pathways of these trans isomers are not fully understood. In the present work, the desaturation and chain elongation of [1-14C]linoleic acid, 9cis,12trans -18:2, 9trans,12cis -18:2, alpha-linolenic acid, 9cis, 12cis,15trans -18:3 and 9trans,12cis, 15cis -18:3 were studied using a perfused rat liver model. After perfusion with both trans isomers of 18:2n-6, the 14C was equally distributed between phospholipids and triacylglycerols, compared to the 70:30 distribution (phospholipids:triacylglycerols) observed after infusing linoleic acid. The corresponding distribution of 14C after perfusion with both trans isomers of 18:3n-3 was comparable to what was obtained for alpha-linolenic acid. The products of conversion were analyzed by combination of different radio chromatographic methods. 9cis,12trans -18:2 was 16 times more converted into a C18:3n-6 fatty acid than linoleic acid into gamma-linolenic acid. Trans -18:2 isomers were more elongated into "dead-end products" when compared to the conversion of linoleic acid into 20:2n-6 (from 2- to 5-times more). 9cis,12cis,15trans -18:3 and 9trans,12cis, 15cis-18:3 were 2- and 10-times less converted to trans -20:5, respectively, than alpha-linolenic acid into eicosapentaenoic acid. Moreover, 9cis,12cis,15trans -18:3 and 9trans, 12cis, 15cis -18:3 were equally and 2.5-times more elongated into "dead-end products", respectively, than alpha-linolenic acid into 20:3n-3. The partitioning of the conversion between formation of desaturated and chain elongated products on the one hand and production of "dead-end products" on the other was also calculated. Compared to their cis analogs, 9trans,12cis -18:2 and 9trans,12cis, 15cis -18:3 were elongated into trans "dead-end products" rather than being converted to desaturated and chain elongated trans-metabolites. On the other hand 9cis,12cis,15trans -18:3 was more desaturated and chain elongated into 17trans 20:5 rather than elongated into 17trans -20:3.