Purpose Intraoperative neurologic monitoring can be useful, but transcranial motor evoked potentials (TcMEPs) are sensitive to anesthetic agents. We compared the effects of anesthetics on the newly developed transesophageal motor evoked potentials (TeMEPs) with those on TcMEPs. Methods Eleven pigs (25.6 +/- 0.8 kg) were anesthetized by desflurane inhalation, remifentanil was maintained at 0.5 mu g/kg/min until the end of the experiment. End-tidal desflurane concentration was then maintained at 7, 4, 10, and 13%, and TcMEPs and TeMEPs were measured at each concentration. Desflurane was then discontinued and propofol was infused at 10, 20, 40, and 60 mg/kg/h, and TcMEPs and TeMEPs were measured at each infusion dose. An electroencephalogram monitor was used to measure the hypnotic level. Results Both desflurane and propofol anesthesia decreased bispectral index in a dose-dependent manner (P < 0.0001), replicating shallow (or adequate) to deep hypnotic levels in both anesthetic methods. The amplitude of TeMEPs was clearly larger than that of TcMEPs and was significantly larger at all anesthetic depths and all limb sites (P < 0.0001). Amplitudes of the lower extremities were lower than those of the upper extremities (P < 0.0001) for both TcMEPs and TeMEPs, but the amplitudes of TeMEPs were sufficiently large under desflurane as under propofol. The trend of concentration-dependent decrease in the amplitudes of TeMEPs under both anesthetics was not as apparent as in that of TcMEPs. Conclusions TeMEPs are more tolerant to anesthesia than TcMEPs and may be a promising MEP monitoring technique for the lower corticospinal tract.