Our objective was to test the hypotheses that conjugated linoleic acid (CLA) and/or tetradecylthioacetic acid (TTA) would have beneficial effects on the nutritional quality of rainbow trout (Oncorhynchus mykiss) through decreased lipid content of flesh or viscera, and increased levels of beneficial fatty acids including accumulation of CLA or TTA themselves. The specific aims of this study were to determine the effects of CLA and TTA on growth performance, lipid and fatty acid metabolism, and selected gene expression in commercial sized trout grown in seawater. Trout were fed for eight weeks on fish meal and fish oil diets containing either 0.5% or 1% CLA, or 0.5% TTA. The effects of the supplemented fatty acids on growth, feed efficiency, lipid contents, class compositions and fatty acid compositions of flesh and liver were determined, along with liver highly unsaturated fatty acid synthesis, activities of key enzymes of fatty acid oxidation in liver and muscle, and expression of carnitine palmitoyltransferase-I (CPT-I) and fatty acyl desaturase and elongase genes. Neither functional fatty acid had any effect on growth parameters, condition factor, viscero-and hepato-somatic indices or fillet colour, and there were no mortalities in any of the treatments. Dietary CLA, but not TTA, decreased the lipid content of liver, but neither fatty acid had any significant effect on lipid class compositions of liver and flesh. Both CLA and TTA were incorporated into tissue lipids, with higher percentages found in flesh compared to liver. In addition, production of hexaene fatty acid by liver microsomes was increased by dietary CLA or TTA, and both functional fatty acids increased the proportion of n-3 fatty acids in liver mainly due to increased 20:5n-3 and 22:6n-3. However, the expression of fatty acyl Δ6 desaturase was significantly lower in fish fed CLA or TTA, whereas the expression of PUFA elongase was increased, significantly so in fish fed 1% CLA. CPT-I activity was increased by TTA in liver and red muscle, and acyl CoA oxidase activity was increased by TTA in liver and CLA at the higher dietary inclusion level in red muscle. There was a clear trend for CPT-I expression to be increased in fish fed 0.5% CLA or TTA in all tissues although this was only significant in white muscle. The results showed that both CLA and TTA had effects on lipid metabolism that partly support the hypotheses tested.Although CLA or TTA did not enhance growth parameters, feed conversion or potential yield, nutritional quality could be enhanced, and sea-run trout fed CLA or TTA could be beneficial in the human diet through provision of bioactive fatty acids, with no detrimental effects on 20:5n-3 or 22:6n-3 levels.3