Previous studies by our group suggest that the neuropathology of autism is characterized by a disturbance of cortical modularity. In this model a decrease in the peripheral neuropil space of affected minicolumns provides for an inhibitory deficit and a readjustment in their signal to noise bias during information processing. In this study we proposed using low frequency transcranial magnetic stimulation (rTMS) as a way increasing the surround inhibition of minicolumns in autism. Thirteen patients (ADOS and ADI-R diagnosed) and equal number of controls participated in the study. Repetitive TMS was delivered at 0.5 Hz, 2 times per week for 3 weeks. Outcome measures based on event-related potentials (ERP), induced gamma activity, and behavioral measures showed significant post-TMS improvement. The results suggest that rTMS offers a potential therapeutic intervention for autism.