Question Artificial modulation of the cerebellar output with repetitive transcranial magnetic stimulation could directly influence the plastic response of the motor cortex that depends on the peripheral input ( Popa et al., 2012 ). Here we investigate the change of the resting-state functional connectivity between the cerebellum, the basal ganglia, the thalamus, and the cortical motor areas before and after the inhibitory rTMS or sham stimulation of the right cerebellar hemisphere. Methods The resting state fMRI of seventeen right-handed healthy subjects (age 26.6 ± 9 years, range: 18–53) was acquired twice at three time points around two types of intervention. The intervention types were either real or sham continuous theta-burst stimulation (cTBS; Huang et al., 2005 ) of the right cerebellar hemisphere, delivered in two different days. The scanning time-points for each day were: baseline, before the intervention, and at 10 min and 60 min after the end of the intervention. The stimulation was aimed at the VIII lobule of the right cerebellar hemisphere ( Popa et al., 2010 ) and delivered at 90% of the active motor threshold. The MRI data was preprocessed with SPM5 ( SPM5, xxxx ) and time series of the signal in selected regions of interest were extracted. The regions of interest were selected in FSLview ( FSLview, xxxx ) as 4 mm-radius spheres around specific coordinates previously defined for circuits involved in motor-skill learning, which are both distinct and connected ( Doyon et al., 2009 ): the cerebello-thalamo-cortical (CTC) loop and the striatio-thalamo-cortical (STC) loop. The integration within a circuit was defined as Ix = −1/2 ln∣Rx∣ and between circuits as Ix/y = 1/2 ln(∣Rx∣. ∣Ry∣/∣Rxy∣), where Rx is the correlation matrix of network X and ∣·∣ stands for the determinant function ( Merrelec et al., 2008 ). The integration was computed for each subject, each stimulation type, each time-point, and every combination of regions/circuits. Results We have found that despite the lack of effect on the integration of the whole motor network, there were significant changes within and between sub-networks: an increase in integration from baseline to10 min after the intervention between the left cortico-cerebellar and the left and right cortico-striatal loops, as well as within the cerebello-thalamo-striatal loops bilaterally. All parameters returned to baseline levels at 60 min after the intervention. Conclusions This demonstrates that inhibitory cerebellar stimulation is actively influencing the connectivity within the motor loops, involving both cortical and subcortical structures. It suggests that the stimulation of one area can potentially change the flow of information throughout the brain, and that the inhibition of cerebellar cortex in particular can enhance the strength of the communication between the cortical motor areas and the basal ganglia.