Previous studies have demonstrated that subthreshold 1 Hz repetitive transcranial magnetic stimulation (rTMS) causes a decrease in corticospinal excitability in neurologically normal subjects. The effects of subthreshold 1 Hz rTMS upon corticospinal excitability and intracortical inhibition in subjects with focal hand dystonia (FHD) is not yet clear. The purpose of this study was to examine the effects of low intensity 1 Hz rTMS upon these variables in control and FHD subjects. We recorded electromyographic (EMG) from the first dorsal interosseous (FDI) muscle of the dominant hands of seven control subjects, and seven affected hands of five FHD subjects. We used single and paired pulse TMS to examine motor evoked potential (MEP) amplitude, short interval intracortical inhibition (ICI) and silent period duration before, during and after 20 min of low intensity 1 Hz rTMS. MEP amplitude decreased significantly over the course of the rTMS in control subjects, but did not change in FHD subjects. Silent period duration was significantly longer in control subjects after rTMS, but there was no change in FHD subjects. There was no significant change in ICI after rTMS in either subject group, despite the rTMS intensity being set to preferentially activate intracortical inhibitory networks. This suggests that low intensity 1 Hz rTMS may have limited application in the normalisation of inhibitory function in FHD.