We studied MEG and fMRI responses to electric median and tibial nerve stimulation in five healthy volunteers. The aim was to compare the results with those of a previous study using only fMRI on the primary and secondary somatosensory cortices in which the somatotopic organization of SII was observed with fMRI. In the present work we focus on the comparison between fMRI activation and MEG equivalent current dipole (ECD) localizations in the SII area. The somatotopic organization of SII was confirmed by MEG, with the upper limb areas located more anteriorly and more inferiorly than the lower limb areas. In addition a substantial consistency of the ECD locations with the areas of fMRI activation was observed, with an average mismatch of about 1 cm. MEG ECDs and fMRI activation areas showed comparable differences in SI.