Few studies have included magnetoencephalography (MEG) when assessing the diagnostic value of presurgical modalities in a nonlesional epilepsy population. Here, we compare single photon emission computed tomography (SPECT), positron emission tomography (PET), video-EEG (VEEG), and MEG, with intracranial EEG (iEEG) to determine the value of individual modalities to surgical decisions. We analyzed 23 adult epilepsy patients with no abnormal MRI findings who had undergone surgical resection. Localization of individual presurgical tests was determined for hemispheric and lobar locations based on visual analysis. Each localization result was compared with the ictal onset zone (IOZ) defined by using iEEG. The highest to the lowest hemispheric concordance rates were MEG (83%) > ictal VEEG (78%) > PET (70%) > ictal SPECT (57%). The highest to lowest lobar concordance rates were ictal VEEG = MEG (65%) > PET (57%) > ictal SPECT (52%). Statistical analysis showed MEG to have a higher hemispheric concordance than that of ictal SPECT (P = 0.031). We analyzed the effects of MEG clustered-area resection on surgical outcome. Patients who had resection of MEG clusters showed a better surgical outcome than those without such resection (P = 0.038). It is suggested that MEG-based localization had the highest concordance with the iEEG-defined IOZ. Furthermore, MEG cluster resection has prognostic significance in predicting surgical outcome.