AbstractSelected ion monitoring was used in conjunction with gas chromatography/mass spectrometry to analyzetert‐butyldimethylsilyl ethers (tert‐BDMS) of 1,2‐diacyl‐sn‐glycerols derived from naturally occurring glycerophospholipids, including those ofEscherichia coli, soybean, egg yolks and porcine liver. First, the fatty acid composition of the unknown glycerophospholipid was determined by gasliquid chromatography (GLC) and, based on that, the fatty acids (mostly >0.5 wt%) were selected for monitoring the characteristic fragmentation ions produced from the fatty acid residues of the correspondingtert‐BDMS derivatives of 1,2‐diacyl‐sn‐glycerols. Next, thetert‐BDMS derivatives were separated by GLC on a 65% methylphenylsilicone gum wall‐coated open‐tubular (WCOT) column according to the degree of unsaturation and the chain length of the fatty acid residues, and then directly introduced into the ion source of the mass spectrometer. The selected fragmentation ions, [RCO+74]+ representative of the fatty acid residues, and [M‐57]+ indicative of the molecular weight of the derivatives, were monitored simultaneously. It thus became possible to determine the molecular species of thetert‐BDMS derivatives by measuring a specific combination of two [RCO+74]+ and an [M‐57]+ ion with the same retention time on the selected ion monitoring (SIM) profile. High background noise caused by volatilization of stationary phase at high temperature was largely overcome by selected ion monitoring. However, the fragmentation ion peaks produced fromtert‐BDMS derivatives of highly unsaturated glycerophospholipids showed a distorted SIM profile, which was attributed to interaction between thetert‐BDMS derivatives and the methylphenylsilicone phase of the column. Use of a WCOT column with a more polar liquid phase is therefore recommended for the analysis of highly unsaturated molecular species.