The present study combined functional magnetoencephalography (MEG) and anatomical magnetic resonance imaging (MRI) information in three patients affected by tuberous sclerosis and partial epilepsy. MEG recordings were performed during both spontaneous and visual evoked activity. The former showed a large variety of complexes whose spatial and temporal distribution suggested different neuronal populations acting simultaneously in the same focal district. When these data were integrated with MRI images (magnetic source imaging, MSI) there was agreement in the definition of tubers and extension of the epileptogenic area. Furthermore, cortical reactivity to rhythmical stimulation was studied with trains of visual stimuli according to a recently proposed frequency responsiveness procedure (FRP). As compared to normal controls, a large 6 Hz activity was observed during the pause after a non-resonant stimulation. This altered resonance property may indicate a disturbed primary sensory processing notwithstanding a preserved associated processing. These results show that neuronal malfunctioning in tuberous sclerosis complex patients may not be restricted to the area of cortical tubers, but can also affect functionally correlated regions.