Gas chromatography (GC) has been a standard analytical tool in lipid chemistry. The rapid attenuated total reflection (ATR) infrared (IR) American Oil Chemists' Society (AOCS) Recommended Practice (Cd 14d-97) was compared to the capillary GC AOCS Recommended Practice (Ce 1f-97) that was optimized to accurately determine total trans fatty acids on highly polar stationary phases. This comparative evaluation was validated in an independent laboratory. These procedures were used to quantitate the total trans fatty acid levels in partially hydrogenated vegetable oils, measured as neat (without solvent) triacylglycerols (TAG) by ATR and as fatty acid methyl ester (FAME) derivatives by capillary GC. Unlike FAME, TAG determination by ATR required no derivatization, but samples had to be melted prior to measurement. Five blind replicates for each of three accuracy standards and three test samples were analyzed by each technique. The GC and ATR determinations were in good agreement. Accuracy was generally high. The ratios of ATR mean trans values (reported as percentage of total TAG) to the true values (based on the amount of trielaidin added gravimetrically) were 0.89, 0.98, and 1.02 for accuracy standards having about 1, 10, and 40% trans levels. The corresponding GC values, determined as percentage of total FAME, were 0.98, 0.99 and 1.04. The ratios of mean trans values determined by these techniques were ATR/GC 0.85, 1.04, and 1.01 for test samples having trans levels of about 0.7, 8, and 38%, respectively. The optimized GC procedure also minimized the expected low bias in trans values due to GC peak overlap found with the GC Official Method Ce 1c-89. Satisfactory repeatability and reproducibility were obtained by both ATR and GC.For several decades analytical methods, such as gas chromatography (GC) (1) and infrared (IR) spectroscopy (2,3), for the determination of total trans fatty acids in partially hydrogenated vegetable oils have each been widely used (4) and repeatedly modified in order to improve accuracy (5,6). A recent publication by Duchateau et al. (5) detailed optimized capillary GC separations on highly polar stationary phases for the accurate determination of trans fatty acids in partially hydrogenated vegetable oils and in refined (deodorized or stripped) oils. This procedure was adopted by the American Oil Chemists' Society (AOCS) as Official Method AOCS Ce 1f-96 (7). The GC Official Method AOCS Ce 1c-89 (1) for partially hydrogenated vegetable oils underestimates some trans C 18 monoene (18:1) positional isomers in favor of cis 18:1 isomers, with which they overlap. Two relatively minor peaks attributed to the trans-12 and trans-13 plus trans-14 18:1 isomers were resolved by the optimized GC procedure (5), and this reportedly improved the accuracy of the GC determination. These two minor peaks (labeled "valley peaks") emerged between those of the major trans 18:1 isomers and the intense cis-9 18:1 peak. In refined vegetable oils monotrans 18:2 and 18:3 isomers occur at levels that can reach 1-3% of tot...