The purpose of this study is to evaluate the difference between anatomical locations of mismatch negativity (MMN) generators using a realistic head model and the Talairach coordinate system. This was performed by dipole source analysis by using a high density 128 channel electroencephalography (EEG) acquisition system and the subjects' individual 3D magnetic resonance images (MRI) for the realistic head model, in 24 healthy subjects. For dipole source localization, both the Talairach coordinate system and the individual MRI realistic head models were used and location results were compared. The MMN generators were clearly localized in the superior temporal gyri, especially in Heschl's gyrus, according to each individual's structural MRI. Only 37.5% of subjects showed the same anatomical locations of the MMN generator in both hemispheres in the realistic head model and in Talairach coordinate system, but fifteen subjects (62.5%) didn't. This result indicates that individually registered functional locations are desirable for the precise localization of activated areas in functional imaging studies and that a brain coordinate system is needed which adequately accounts for ethnic differences.