Trans-vaccenic acid (TVA) is a natural trans fatty acid found in ruminant food produce. It is converted to the cis-9, trans-11 isomer of conjugated linoleic acid (c9, t11-CLA) by the action of stearoyl-CoA desaturase (SCD) in tissue. c9, t11-CLA has been associated with anti-inflammatory effects and also affects lipid metabolism. The aim of the present study was to determine if TVA is bioconverted to c9, t11-CLA in intestinal epithelial cells and to ascertain whether TVA has effects similar to c9, t11-CLA on markers of inflammation relevant to inflammatory bowel disease. The present study demonstrated that TVA treatment led to significant bioconversion into c9, t11-CLA in Caco-2 cells. Treatment with both TVA and c9, t11-CLA resulted in alteration of cellular fatty acid profile and SCD activity in the Caco-2 cell line. However, CLA, but not TVA, significantly modulated transcription of TNF-alpha, IL-12, IL-6 and production of IL-12 by these cells. Thus the present study established that TVA treatment can alter SCD desaturation indices and induce compositional changes in the fatty acid profile of the Caco-2 cell model of the human intestinal epithelium but this is not associated with functional effects on markers of the inflammatory response.