Repetitive transcranial magnetic stimulation (rTMS) shows promise as a treatment for various movement and psychiatric disorders. Just how rTMS may have persistent effects on cortical function remains unclear. We hypothesised that it may act by modulating cortico-cortical and interhemispheric connectivity. To this end we assessed cortico-cortical and interhemispheric coherence before and after low frequency, subthreshold rTMS of the left motor cortex.