An ionic liquid (IL) 111 column was compared with other commonly employed stationary phases including polydimethyl siloxane and polyethylene glycol for the separation of fatty acid monomethyl and dimethyl esters. The fatty acid esters employed in this study were derived from metathesis reactions of vegetable oils both with and without olefins. The IL 111 column demonstrated enhanced performance compared with conventional columns for the separation of these esters. These advantages included significantly enhanced retention of dimethyl esters relative to monomethyl esters, excellent cis/trans isomer separation and the ability to analyze higher carbon number dimethyl esters. As a result, these columns are highly suited for the analysis of mixtures of mono- and dimethyl fatty acid esters found in lipid metathesis reaction products or to determine monofunctional impurities in samples of commercial dimethyl esters.