While conjugated vegetable oils are currently used as additives in the drying agents of oils and paints, they are also attractive molecules for making bio-plastics. Moreover, conjugated oils will soon be accepted as nutritional additives for “functional food” products. While current manufacture of conjugated vegetable oils or conjugated linoleic acids (CLAs) uses a homogeneous base as isomerisation catalyst, a heterogeneous alternative is not available today. This contribution presents the direct production of CLAs over Ru supported on different zeolites, varying in topology (ZSM-5, BETA, Y), Si/Al ratio and countercation (H+, Na+, Cs+). Ru/Cs-USY, with a Si/Al ratio of 40, was identified as the most active and selective catalyst for isomerisation of methyl linoleate (cis-9,cis-12 (C18:2)) to CLA at 165 °C. Interestingly, no hydrogen pre-treatment of the catalyst or addition of hydrogen donors is required to achieve industrially relevant isomerisation productivities, namely, 0.7 g of CLA per litre of solvent per minute. Moreover, the biologically most active CLA isomers, namely, cis-9,trans-11, trans-10,cis-12 and trans-9,trans-11, were the main products, especially at low catalyst concentrations. Ex situ physicochemical characterisation with CO chemisorption, extended X-ray absorption fine structure measurements, transmission electron microscopy analysis, and temperature-programmed oxidation reveals the presence of highly dispersed RuO2 species in Ru/Cs-USY(40).