Abstract The fatty acid composition of fats and oils is commonly determined by gas chromatography after preparing fatty acid methyl esters (FAME). Capillary columns coated with polyethylene glycol emerged as the preferred separation tool for the quantification of the polyunsaturated fatty acids contained primarily in marine oils. However, their selectivity is inadequate for measuring the trans fatty acids (TFA) contained in refined vegetable oils, dairy fats, and marine oils. Highly polar 100% poly(biscyanopropyl siloxane) capillary columns provide the necessary selectivity, but small differences in the phase polarity caused by column age, conditioning, or manufacturing variations affect the reproducibility of their separations of these complex samples. In this study, a simple procedure is described to compensate for small variations in column selectivity by adjusting the elution temperature. The balance between the dipole-induced dipole interactions and dispersive interactions was determined by measuring selectivity factors [SF(i)] corresponding to the elution of an unsaturated FAME such as 18:3n-3 relative to two saturated FAME such as 20:0 and 22:0. Knowing the SF(i) provided by the installed capillary column at a given elution temperature, and the SF(i) of the target separation, we propose a simple calculation to determine the necessary elution temperature adjustment to achieve (or restore) the desired separation. After determining the SF(i) which provides the optimal separation of TFA, the novel methodology was applied to the separation of refined vegetable oils, butter fats, and marine oils.