This study reports methods for the quantitative determination of stable isotope-labeled essential fatty acids (EFAs) as well as an experiment in which deuterium-labeled linoleic acid (18:2n-6) and ␣ -linolenic acid (18:3n-3) were compared with those labeled with carbon-13 in rat plasma in vivo. Standard curves were constructed to compensate for concentration and plasma matrix effects. It was observed that endogenous pools of fatty acids had a greater suppressing effect on the measurements of 13 C-U-labeled EFAs relative to those labeled with 2 H 5 . Using these methods, the in vivo metabolism of orally administered deuterated-linolenate, 13 C-U-labeled linolenate, deuterated-linoleate, and 13 C-U-labeled linoleate was compared in adult rats (n ؍ 11). There were no significant differences in the concentrations of the 2 H versus 13 C isotopomers of 18:2n-6, 18:3n-3, arachidonic acid (20:4n-6), and docosahexaenoic acid (22:6n-3) in rat plasma samples at 24 h after dosing. Thus, there appears to be little isotope effect for 2 H 5 -versus 13 C-U-labeled EFAs when the data are calculated using the conventional standard curves and corrected for endogenous fatty acid pool size and matrix effects. In essential fatty acid (EFA) metabolic studies, 2 H and 13 C are the most commonly used stable isotopic atoms in tracer studies (1-6) since their discovery (7, 8) and application to metabolic studies about 70 years ago (9). Compared with 2 H, the 13 C atom has a relatively small difference in mass with respect to 12 C and so is very similar in its physicochemical characteristics. For 13 C-labeled fatty acids, a high-precision gas chromatography-combustion isotope ratio mass spectrometric system could detect 13 C in fatty acids at very low signal levels, down to 3 pmol per injection (10). 2 H-labeled fatty acids were used extensively and measured by GC-MS in electron impact (11), positive chemical ionization (12), and negative chemical ionization (NCI) (13) in biological samples. Other non-mass spectrometry methods, such as conventional GC with a flame ionization detector (FID), could be applied when the deuterated fatty acids had enough mass difference to be chromatographically resolved (13-15) and when sufficient amounts occurred in biological experiments such that they could be adequately detected (15-17). However, for fatty acids, no direct comparisons have been made between the metabolic behavior of 2 H and 13 C tracers either in vitro or in vivo.In the course of performing measurements of human (18) and rat (19) plasma samples containing multiple stable isotopes, it became apparent that there were several analytical difficulties. The plasma matrix exerted a suppressing effect on the fatty acid isotopic signals as measured in the NCI mode. This suppression was greater for the 13 C signals relative to those of the same fatty acid labeled with 2 H. Therefore, standard curves for the various fatty acid isotopes to be used were required. In addition, methods were required for estimating the responses of fatty acid m...