The neuroimaging techniques of magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI) measure different aspects of brain activity. MEG and electroencephalography (EEG) reflect extracranial measures of time-resolved neuromagnetic fields or potentials whereas fMRI displays tomographically hemodynamic changes in response to neuronal activation. EEG and fMRI can be recorded simultaneously and can provide basic knowledge on the relation of the two mechanisms of signal generation. MEG is less prone to spatial distortions and, thus, may be better mapped to the tomographic images. From the beginning of the 1990s, investigations involving both modalities with the same paradigm were presented regularly. Many of these studies investigated localization properties of both systems for presurgical localization. Comparative measurements showed largely similar activation patterns in sensory, motor, and cognitive tasks. The difference between fMRI and MEG coordinates of the activations to the same task, commonly show deviations of 1 cm or more (about 2 cm with EEG). However, the differences in both modalities may distinguish in hemispheric lateralization, signal dynamics, or effects of disorders. We suggest that in addition to the integrative use of the modalities, a complementing use of MEG or EEG and fMRI may lead to new measures which help to understand brain physiology and mechanisms of neuronal dysfunctions.