The localization of human hand primary motor area (M1) has been the object of several studies during the last decades. EEG source analysis, functional magnetic resonance imaging (fMRI) and focal transcranial magnetic stimulation (TMS) are non-invasive methods for localizing M1 with good accuracy compared to direct electrocorticography (ECoG) results. EEG sources were reconstructed with Cortical Current Density (CCD) method, allowing to evaluate simultaneous and distributed patterns of activation and to increase accuracy by constraining on information derived from fMRI (fMRI-CCD). The aim of this study was to compare the M1 contribution of movement-related cortical potentials (MRCP) with TMS and fMRI results and to test the effect of constraints strength, algorithm norm and localization methods over CCD reconstruction. Seven right-handed healthy subjects underwent 64-channel EEG recording of MRCP to right thumb movement, focal TMS mapping of the right abductor pollicis brevis muscle and fMRI during right hand movement. We found fMRI activations, EEG sources and TMS mapping corresponding to the anatomical landmark of the hand area in all subjects with fMRI and TMS center-of-gravity and in almost all subjects using fMRI-CCD with moderate constraint. A significant improvement was found using fMRI-CCD compared to CCD alone. This study confirms the usefulness of multimodal integration of fMRI, EEG and TMS in localizing M1 and the possibility to increase EEG spatial resolution using fMRI information.