Scientific research over the last two decades has demonstrated relationships between dietary intake of certain fatty acids (FA) with double bonds in the trans configuration in their alkyl chain (trans fatty acids, TFA), and the development of severe metabolic or cardiovascular diseases such as arteriosclerosis, hypertension and diabetes mellitus type-2 (Mozaffarian et. al 2006 & 2009). In response to such findings, several countries including Denmark, Canada and the United States have implemented regulations regarding limitation and labelling of TFA content of fats, oils, foods and dietary supplements. Recent studies have shown that intake of TFA with different chemical structures results in different metabolic and health effects. Dietary intake of c9,t11-18:2 and its biological precursor t11-18:1 (vaccenic acid) has been credited with positive health effects [Field et al., 2009]. In contrast, consumption of dietary t10,c12-18:2 has been associated with hyperinsulinemia and fatty liver in mouse studies [Clément et. al 2002]. However, a critical common limitation of these studies has been the availability of authentic reference materials and appropriate analytical methods to quantify the subject TFA and their metabolites. Organic synthesis of the possible FA isomers involved can play a key role in the correct identification and analysis of these TFA. Misidentification of analytes can lead to an incorrect evaluation of the health effects associated with specific FA, and therefore pure and well-characterized reference materials are essential. A classic case was reported when an overestimation of trans-16:1 isomers due to inadequate separation techniques resulted in an association of these isomers with coronary heart disease [Precht et al., 2000a]. It is interesting to note that trans-16:1n-7 has also been associated with lower insulin resistance [Mozaffarian et al., 2010]. A clear identification of the trans-16:1 isomers is definitely required in order to understand its biological significance.