Analytical parameters and quality control measures were optimized for standard direct gas chromatographic (GC) analysis of trans fat in unlabeled bakery products, and differences in concentrations measured in samples assayed with and without the modifications were evaluated. Total lipid was extracted with chloroform/methanol from homogenized cakes, cookies, doughnuts, pastries, muffins, and commercially available reference materials (NIST SRM 2387 Peanut Butter, LGC7103 Sweet Digestive Biscuit). Total lipid was saponified and fatty acids were derivatized to methyl esters (FAME) and analyzed by GC using a 100% nonbonded bis-cyanopropyl polysiloxane column (100 m×0.25 mm, 0.2 µm film). Total FAME entering GC was optimized to separate C18:1-12t and C18:1-13t isomers that occur at a significant level but often remain unresolved from the C18:1-9c peak in products containing partially hydrogenated vegetable oils. Silver-ion solid-phase extraction was used to validate identification of the major C18:1 cis/trans peaks. For samples assayed by the standard method and with specific sample-to-sample quality control and GC optimization, the former underestimated trans fat by 2 to 5 g/100 g (0.2-0.6 g/serving) in some products. Differences were less for foods containing <1 g/100 g, but nonetheless could have implications for labeling because trans fat levels <0.5 g/serving may be declared zero according to U.S. Food and Drug Administration regulations. The practical modifications and controls described can be implemented in routine standard GC analysis to increase the consistency and validity of trans fat measurement across a range of samples with unknown fat content and fatty acid composition.