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3-Hydroxy fatty acids (3-OHFAs), components of lipid A of gram-negative bacteria are useful chemical markers of endotoxin.We analyzed 3-OHFAs in house dust as trimethylsilyl (TMS) methyl ester derivatives in the electron impact ionization mode using gas chromatography ion-trap mass spectrometry. Linear calibrations with r > 0.995 were observed for all the 3-OHFA methyl ester external standards.Recovery efficiency experiments with house dust demonstrated that accurate quantification requires calibration curves to be subjected to phase separation and solid phase extraction (SPE) because of differing clean-up losses according to chain length of 3-OHFAs. Recovery experiments also demonstrated interference with detection of C16:0 by the ion trap, which may be due to suppression of ionization by a constituent in house dust. Interference was overcome by injecting 1:4 dilutions of derivatized samples. The range of recoveries was 89.3%—111.5% for 3-OHFAs added to house dust. The reproducibility of injections was high (CV for C14:0 = 2.36%). The limit of detection (LOD) was 0.15 ng/mg for each 3-OHFA.The modifications we made included: use of 3-hydroxy C11:0 and C13:0 methyl esters as internal standards, subjecting calibration standards to phase separation and SPE; addition of water to phase separation; addition of 1-pentadecanol as a carrier; injecting 1:4 diluted TMS derivatives of 3-OHFAs; and monitoring both m/z 131 and 133 ions to improve stability of area measurements for product ions. This method of optimization establishes an appropriate technique for quantification of 3-OHFAs in house dust.