Gas chromatography using a highly polar column combined with field ionization mass spectrometry (FI-MS) is used as a comprehensive two-dimensional (2D) separation approach to analyze mixtures of fatty acid methyl esters (FAMEs). A unique ordered pattern and classification of FAMEs is obtained in a 2D GC × FI-MS separation plot based on the number of carbons, the degree of unsaturation, and a combination of both by which the geometrical, positional, and structural isomers group together. FAMEs with different chain length but identical geometry, position, and degree of unsaturation follow linear patterns. These subclassifications (linear functions) can provide information about the geometry, position, and structure of unsaturation of an unknown FAME. Non-FAMEs and FAMEs with different functional groups are identified using the ordered separation pattern of the FAMEs in the GC × FI-MS plot and the exact mass data from the FI-MS mode. Measurement of exact mass also acts as a high-resolution separation technique to separate overlapping peaks. The method is illustrated by application to samples of fish, canola, and biodiesel oils and standard mixtures of 37 FAMEs and of α-linolenic acid methyl ester geometrical isomers. A great wealth of information is achieved in a single run.