Purification and analysis of very small quantities of arachidonic acid lipoxygenase products from biological samples remains a challenging task. Gas chromatography-mass spectrometry is an ideally suited technique unsurpassed in the analytical figures of merit of sensitivity, specificity, and accuracy for the quantitation of such hydroxy lipids as 5-hydroxyeicosatetraenoic acid and the LTB4 isomers. We have developed procedures to incorporate oxygen-18 into the carboxyl moiety of these fatty acids as well as 12-hydroxyl position of LTB4 and report on the suitability of these isotopimers as internal standards for quantitative mass spectrometry. Furthermore, the enhanced sensitivity of negative ion chemical ionization of the pentafluorobenzyl ester, trimethylsilyl ether derivatives has been examined. The most abundant ion obtained by this technique is the carboxylate anion which retains all oxygen atoms of these eicosanoids. Comparison of the positive electron impact and negative ion CI mass spectrometric behavior is presented.