Question Depending on the frequency of rTMS protocols, previous combined EEG-rTMS-studies have shown different effects on the cortical excitability. Regarding conventional repetitive protocols, facilitation was observed after high frequency stimulation, whereas inhibition on cortical activity was shown after the application of low frequency protocols. Despite conclusions about the direction of rTMS effects, the after rTMS-effects where mainly observed in Event Related Potential (ERP)-studies. The results of oscillatory EEG studies are much more non-uniform, and still remain uncertainty about the nature of after rTMS effects on quantitative EEG measures, because of different rTMS protocols including high variability of experimental conditions such as investigated subjects (healthy probands versus patients), stimulation location, rTMS parameters and EEG-measure procedures. In this study we analyzed the frequency dependent effects of rTMS over the right dorsolateral prefrontal cortex (DLPFC) on the quantitative EEG in healthy female subjects. We preferred the right frontal stimulation regarding the prior findings in reduction of anxiety and depressive symptoms. Additionally we analyzed connectivity pattern in the default mode network (DMN). Our hypothesis was, that the right frontal low frequency rTMS inhibities cortical activity. Furthermore, we included behavioral measures to measure the interaction of rTMS with affective state. Methods Twenty out of 40 healthy female subjects received one session of 1 Hz rTMS on the right DLPFC, 20 subjects one session of 10 Hz rTMS. In a cross over design a placebo stimulation was applied two weeks later. Pre and post rTMS a 10 min resting state EEG was analyzed. After artefact control we used sLORETA (standardized low-resolution brain electromagnetic tomography), in order to analyse the three dimensional cortical distribution of electrical current density for the main EEG frequency bands. For behavioral measures we used the Beck Depression Inventar (BDI) questionaire as instrument for affective trait markers and the Multidimensional Mental State Measure Questionaire (German MDBF). Results After 1 Hz rTMS a reduction of temporal theta EEG activity ipsilaterally to the stimulation side was observed. In the DMN, after high frequency rTMS an increase of connectivity in alpha-band and after low frequency rTMS a decrease of beta activity, both between medial prefrontal cotex and left inferior parietal lobule, was found. Furthermore, an increase of frontal alpha-assymmetry towards left hemisphere after 1 Hz rTMS could be shown in participants with higher baseline BDI-scores. Clinically relevant changes of mood, however, were not present. Conclusions Both rTMS protocols have shown a modulating effect on the activity of the DMN in healthy females. In order to get more conclusions about translative rTMS effects on behavior, further analysis including more precise behavioral measures are necessary.