Major Depressive Disorder (MDD) is a common psychiatric disorder that represents one of the main public health problems worldwide. It has been projected that for 2020 it will be the second cause of disability-adjusted life years just below ischemic heart disease. Quantitative electroencephalogram provides the opportunity to study cortical oscillatory activity across the different frequency bands. It constitutes an accessible tool to explore the clinical and neurophysiologic correlates underlying psychiatric disorders as well as the effect of diverse therapeutic options and the performance through cognitive tasks. Repetitive transcranial magnetic stimulation is a technique that allows the stimulation of the cerebral cortex noninvasively, relatively painlessly and with fairly few side effects. The vast majority of rTMS studies target left dorsolateral prefrontal cortex (DLPFC) based on imaging studies showing that left prefrontal cortex dysfunction is pathophysiologically linked to depression. However, there is some evidence implicating right PFC in the pathophysiology of depression. Comparison of antidepressant efficacy of diverse stimulation frequencies is relevant since a main concern around rTMS is its potential to induce seizures; hence we consider that frequency of stimulation is an important aspect to be studied. For this study we aimed to elucidate the clinical efficacy of rTMS comparing two groups of depressed patients stimulated over DLPFC, one over the left (at 5 Hz) and other over the right (at 1 Hz). We also meant to know if there were clinical and electroencephalographic differential long-term after-effects between those groups of treatment. We included twenty right-handed patients with a DSM-IVR diagnosis of MDD. They were assigned into two groups of treatment. Group 1 received 5Hz rTMS over the left DLPFC. Group 2 received 1Hz rTMS over the right DLPFC. We obtained two EEG measurements in order to analyze Z score of broad-band spectral parameters and cross-spectral. No statistical differences among groups were found in response to treatment after weekly comparisons of clinimetric scores and significant differences between baseline and final assessment by HDRS, MADRS, BDI and HARS. The major rTMS effect on EEG was observed in the group that received 1 Hz over the right DLPFC and no significant effects were observed for the group that received 5 Hz over the left DLPFC. Our results propose that administration of 15 sessions on either left (5 Hz) or right (1 Hz) rTMS over DLPFC is sufficient to reach response to treatment, assessed by HDRS, MADRS, BDI and HARS in subjects with MDD. Moreover, in both cases rTMS was able to induce an equivalent antidepressant effect. The major effect of rTMS on EEG was observed in the right 1 Hz rTMS group where changes were elicited mainly over frontal, central and temporal regions on alpha and particularly beta frequency bands. In a lesser extent for left 5 Hz rTMS group the main effect was observed on anterior regions for beta and particularly alpha frequency bands. We believe it is pertinent to continue exploring the therapeutic potential of lower stimulation frequencies, for what further research including larger samples is still necessary to confirm these trends.