Transcranial Magnetic Stimulation (TMS) is a safe noninvasive technique to modulate cortical excitability. The introduction of repetitive TMS (rTMS) provides a new tool for studying psychopathologic disorders and higher cognitive functions. One of the most salient potential effects of rTMS is its possible therapeutic effect on different psychiatric disorders like depression, mania, obsessive compulsive disorder, post-traumatic stress disorder and schizophrenia. The mechanisms by which exerts its therapeutic effects are still unknown. However, the combination of this new methodology with functional neuroimaging techniques may help clarify what cerebral dysfunctions underly certain psychiatric conditions at the same time that it provides novel insights into brain cortico-cortical and cortico-subcortical connectivity.