Some plant oils contain non-methylene-interrupted polyunsaturated fatty acids (NMIFAs). Pinolenic acid (all cis Δ-5,9,12/18:3) and columbinic acid ( trans,cis,cis Δ-5,9,12/18:3) are NMIFAs that exist in pine seed oil and columbine seed oil, respectively. We investigated the double bond position of fatty acid recognized by the fatty acid chain elongation system (FACES) of rat liver using NMIFAs as experimental tools. In the total elongation assay, amounts of C2 unit chain-elongated metabolites of pinolenic acid and columbinic acid were 32% and 11%, respectively, compared to that of γ-linolenic (all cis Δ-6,9,12/18:3) as the substrate. In the condensation reaction assay, the rate limiting step of FACES, the conversion rates of pinolenic acid and columbinic acid to the corresponding C20 β-keto fatty acids were 19% and 9% of that of γ-linolenic acid, respectively. The formation of elongated metabolite of podocarpic acid (all cis Δ-5,11,14/20:3) was only 7% of that of arachidonic acid (all cis Δ-5,8,11,14/20:4). From these results it was concluded that the condensing enzyme of FACES could recognize the methylene-interrupted cis double bond structure vicinal to the carboxyl group in the fatty acid molecule.