We compared the effect on reaction times of transient interference with function of the dorsal premotor cortex (PMd) using a pair (25-ms interval) of transcranial magnetic stimulation (TMS) pulses with long-term interference produced by a new repetitive TMS paradigm known as "theta burst stimulation" (TBS). Pairs of TMS pulses over left PMd increased choice but not simple reaction times of the right hand if given at the onset of the reaction interval. There was no effect of stimulation over right PMd or at a midline parietal control site (Pz). In contrast, TBS over either left or right PMd increased choice RTs of both hands for at least 5-10 min after the end of TBS. Pairs of TMS pulses over left PMd also increased error rates whereas TBS had no effect on error rates despite the effect on RTs. We suggest that TBS leads to widespread changes in activity and more complex effects on behaviour than expected from the paired pulse TMS and conclude that transient and long-term forms of interference with function may influence behavioural tasks in subtly different ways.