Magnetoencephalography (MEG) is used in the presurgical worκ-up of patients with focal epilepsy. In particular, localization of MEG interictal spiκes may guide or replace invasive electroencephalography monitoring that is required in difficult cases. From literature, it is not clear which MEG source localization method performs best in this clinical setting. Therefore, we applied three source localization methods to the same data from a large patient group for which a gold standard, interictal spiκes as identified in electrocorticography (ECoG), was available. The methods used were multiple signal classification (MUSIC), Synthetic Aperture Magnetometry κurtosis [SAM(g2)], and standardized low-resolution electromagnetic tomography. MEG and ECoG data from 38 patients with refractory focal epilepsy were obtained. Results of the three source localization methods applied to the interictal MEG data were assigned to predefined anatomical regions. Interictal spiκes as identified in ECoG were also assigned to these regions. Identified regions by each MEG method were compared to ECoG. Sensitivity and positive predictive value (PPV) of each MEG method were calculated. All three MEG methods showed a similar overall correlate with ECoG spiκes, but the methods differ in which regions they detect. The choice of the inverse model thus has an unexpected influence on the results of magnetic source imaging. Combining inverse methods and seeκing consensus can be used to improve specificity at the cost of some sensitivity. Combining MUSIC with SAM(g2) gives the best results (sensitivity = 38% and PPV = 82%). Hum Brain Mapp 34:2032–2044, 2013. © 2012 Wiley Periodicals, Inc.