Fatty acid methyl esters from various fats and oils were separated by comprehensive two-dimensional supercritical fluid chromatography with conventional packed columns and FID detection. The first dimension was a silica gel column and the second dimension was an ODS column. This combination was largely orthogonal for the separation of fatty acid methyl esters. The first dimension separations were primarily based on the number of double bonds while the second dimension separations were based on the chain length. The highly-ordered chromatograms and improved resolution allowed the easy detection and identification of minor components. Although the first dimension separations were performed under isobaric conditions where the peak width increased in proportion to the retention, the programming of the sampling duration allowed us to maintain the optimum re-injection frequency (3-4 times) per peak into the second dimension and so to minimize the total analysis time without deteriorating the resolution.