The technique of comprehensive GC (GC × GC) was applied to the analysis of a standard mixture of FAME. The methodology involved the use of two directly coupled capillary GC columns providing different retention mechanisms, with a pulsing modulator located near their union. The first column was chosen to elute analytes based on b.p. variations, and the second column was based on polarity. Thus, the separation in the two dimensions was orthogonal, since solutes delivered simultaneously to the second column had similar b.p., and the second column separated these primarily on their differentiating mechanisms of polarity. Greater sensitivity of detection and narrower peak widths were obtained; here, peak response increases of about 20-fold were obtained, with pulsed peak widths of about 150 ms. Peaks were displayed in a 2-D contour plot to allow the complexity of the compounds to be seen and their b.p. and polarity properties to be readily recognized. Chromatographic separation of geometric and positional isomers of FAME in the 2-D space is possible. Since retention can be related to the degree and manner of unsaturation and isomerization, and as peak positions are highly reproducible in the 2-D retention map, this is a useful aid for component identification in the absence of appropriate standards. In this work, two column combinations were used to examine the effects of polarity changes on component separation. Improved quantitation based on FID area measurement was demonstrated. A sample of marine oil gave 49 resolved, identified peaks, with at least an additional 20 peaks resolved but not identified.