Introduction High frequency repetitive transcranial magnetic stimulation (HF-rTMS) has gained great interest in multiple clinical and research fields. With HF-rTMS a coil – wherein an alternating current is running – is placed on top of the skull, creating a magnetic field that influences the perpendicular neural tissue, thereby stimulating the neuronal activity of the targeted cortical area [1]. Although it is believed that HF-rTMS accomplishes its effect by influencing entire neuronal networks [2]. One cortical area frequently chosen as stimulation target is the dorsolateral prefrontal cortex (dlPFC), as it is part of the control network. However, despite its popularity and frequent use, very little is known about the differential effect of HF-rTMS over the left and right dlPFC on intrinsic functional connectivity networks in healthy individuals. Therefore the current study will address this issue. Methods The current study assessed the differential effects of left or right dlPFC HF-rTMS (corrected for sham) on intrinsic functional connectivity networks in a sample of 45 healthy individuals. The study was a randomized, single-blind trial with two sessions. During the first session demographic data were obtained and a baseline resting state functional magnetic resonance imaging (rsfMRI) scan was performed. During the second session subjects were randomized to either sham dlPFC HF-rTMS (n=15), left active dlPFC HF-rTMS (n=15) or right active dlPFC HF-rTMS (n=15) directly followed by a second rsfMRI scan. A HF-rTMS session consisted of sixty trains of 5 seconds at a frequency of 10Hz. During the sham condition the coil was tilted 90 degrees relative to the skull. This condition was used in order to correct for time and placebo effects. Independent Component Analysis (ICA) were performed to assess baseline differences and stimulation effects on within and between network functional connectivity. The five components of interest were the left frontal parietal network, right frontal parietal network, default mode network, salience network and reward network. Results The three stimulation groups did not differ on within as well as between functional connectivity of the five components of interest at baseline. Regarding the stimulation effects on within network connectivity, stimulation of the left dlPFC resulted in decreased functional connectivity in the salience network whereas right dlPFC stimulation resulted in increased functional connectivity within this network. Regarding the stimulation effects on between network connectivity, no differences between left or right dlPFC stimulation were found. Discussion Stimulation of either the left or the right dlPFC (compared to sham stimulation) thus seems to lead to opposite effects within the salience network. Since the role of this network in directing attention between internal and external processes [3], and decreased functional connectivity is associated with worsened cognitive functioning in aging [4], the results of this study might have implications for the clinical effects of HF-rTMS over the dlPFC. Therefore future (clinical) studies should implement questionnaires and/ or neurocognitive tasks in order to be able to relate changes in functional connectivity to changes in cognitive functioning.