Low-energy collision-induced dissociation (CID) of the molecular ions of fatty acid methyl esters obtained by electron ionization (70 eV) decompose in the tandem quadrupole mass spectrometer to yield a regular homologous series of carbomethoxy ions. Even at energies up to 200 eV (E lab), primarily carbomethoxy ions are present, with the most abundant found at m/z 101 at hi her energies. The lack of any other CID ions, including m/z 74 (McLafferty rearrangement) or m/z 87, suggest a rearranged molecular ion structure on leaving the first quadrupole mass analyzer. Analyses of various stable isotope variants support the hypothesis of alkyl radical migration to the carboxy carbonyl oxygen atom, with subsequent radical site directed cleavage either with or without a cyclization event. Decomposition of the molecular ions (70 eV) of several methyl branched fatty acid methyl esters, including phytanic acid, iso-methyl and anteiso-methyl branched acids, and tuberculostearic acid, reveals enhanced radical site cleavage at the alkyl branching positions. This method can be used to readily determine methyl (or alkyl) branching positions in a saturated fatty acid methyl ester.