RATIONALE Fatty acids (FA) labeled with 18O at the carboxyl group, including oxidized species (FA18O), are a useful, low-cost, and easy to prepare tool for quantitative and qualitative mass spectrometry (MS) analysis in biological systems. In addition, they are used to trace the fate of FAs in metabolic pathways including FA re-esterification and lipid remodeling pathways. Although a rapid 18O exchange on FA18O in biological systems has been reported, the mechanism contributing to 18O exchange has not been fully evaluated. This gap in knowledge limits the use of FA18O as a standard for MS and complicates data interpretation for FA metabolism in biological systems. METHODS In the present study we have addressed a number of possible mechanisms for a rapid 18O exchange on prostaglandin E2 (PGE2) using rat plasma as a model. High-performance liquid chromatography coupled with electrospray ionization triple quadrupole MS in the multiple reaction monitoring mode was used for quantification. RESULTS The major mechanism for a rapid 18O exchange on PGE218O in rat plasma is PGE2 processing with esterases, while FA re-esterification and non-enzymatic mechanisms do not significantly contribute to this phenomenon. In addition, we report a highly effective inhibition of 18O exchange with diethylumbelliferyl phosphate that can be used to stabilize FA18O in biological samples. CONCLUSIONS These data indicate the necessity to consider esterase activity when FA18O are used to study FA metabolism, and the importance of esterase activity inhibition when FA18O are used as internal standards for MS analysis in biological systems. In addition, the results provide a rational for the development of new approaches to study esterase activities and affinity towards modified FA. Copyright (c) 2012 John Wiley & Sons, Ltd.