BACKGROUND The effects of transcutaneous electric nerve stimulation (TENS) and electroacupuncture (EA) on the cerebral cortex are largely unclear. The purpose of the present study was to investigate the effect of TENS and EA on the cerebral cortex by examining their effect on the median nerve-somatosensory evoked potentials (MN-SEPs). METHODS Twenty volunteers were studied. The cortical and cervical spinal potentials were recorded by median nerve stimulation at the left wrist. Sham TENS, 2 Hz TENS and 2 Hz EA were applied to both ST36 and ST37. MN-SEPs were recorded during sham TENS, 2 Hz TENS and 2 Hz EA, with at least 1 week interval for each subject. One-way analysis of variance was used to determine the differences in latency and amplitude of the MN-SEPs observed in the stimulation and post-stimulation periods compared with baseline. Scheffe's post hoc correction was employed to identify pairwise differences. RESULTS No differences in mean latency were found between the stimulation procedures during the stimulation and post-stimulation periods. 2 Hz EA but not sham TENS or 2 Hz TENS caused higher mean amplitudes in N20 and N30 during the stimulation and post-stimulation periods. CONCLUSIONS EA, but not TENS, induces changes in certain components of the signal.