A 13C NMR approach was taken to study the biotransformation of (R)- and (S)-[2-13C,2-2H]ibuprofen-CoA in isolated rat liver mitochondria. The 13C chemical shift induced by 2H substitution for the C-2 of [2-13C,2-2H]-ibuprofen-CoA is about 0.5 ppm relative to the corresponding 1H-bearing thioester. The C-2 resonances for [2-13C]- and [2-13C,2-2H]ibuprofen-CoA are 5 ppm downfield with respect to their acid counterparts. Consequently, this technique permits real time analyses of the metabolic fate of the doubly labeled substrate in a quantitative manner. The initial rate of the epimerization of (S)-[2-13C,2-2H]ibuprofen-CoA relative to the (R)-counterpart by intact mitochondria was estimated to be 1.5, which is in line with the equilibrium constant determined with the purified epimerase. Contrary to the reports by other groups, this 13C NMR study did not find spontaneous hydrolysis of the CoA-thioester upon being exposed to intact mitochondria. Current focus of this investigation is to extend this NMR methodology to the levels of whole cells and live animals to gain a better understanding of the enantioselective metabolism of ibuprofen.