OBJECTIVE: To explore the clinical application value and feasibility of magnetoencephalography (MEG) in the localization of epileptogenic zone, as compared with scalp electroencephalography. METHODS: 69 patients were enrolled in this study, all the patients were examined with MEG and scalp EEG and received operative treatment. During the operation the patients underwent ECoG and deep EEG monitoring and after the operation the follow-up continued 2 - 3 years. Results were evaluated with Engel curative effect grading. RESULTS: Among the 69 patients there was 62 patients whose localization were limited to one lobe with MEG; while only 30 with EEG. We used Engels, grading to define the effectiveness of the operation. 57 among the 69 patients had effective results with an effective rate of 82.61%. When the lateralization of epileptogenic zone in these 57 patients was counted, the concordance rate of preoperative MEG and EEG with intraoperative EEG was 92.98% (53/57) and 33.33% (19/57) respectively with significant difference between MEG and EEG statistically (chi(2) = 30.250, P = 0.000). The scalp EEG of 34 patients with temporal lobe epilepsy showed bilateral temporal lobe epileptiform discharges or generalized spikes, while the epileptogenic foci were shown with MEG only unilaterally and confirmed by operation finally. CONCLUSIONS: MEG shows significant value in the lateralization of epileptogenic zone of temporal lobe epilepsy. MEG, with a higher time resolution and space resolution, can help to identify epileptogenic zone and mirror foci. MEG can clarify the spatial relationship between the irritative zone and structural lesions or functional areas.