Background Optimising stimulus parameters is important in maximising the efficacy of repetitive transcranial magnetic stimulation (rTMS) in treatment applications. RTMS over motor cortex has been reported as more effective in producing corticospinal inhibition when a monophasic rather than a biphasic stimulus waveform is used. However, non-optimal coil orientation and high intensities of monophasic rTMS may have influenced previous results. Methods In eight healthy subjects, we measured motor evoked potentials (MEPs) in a hand muscle after monophasic and biphasic rTMS (1 Hz for 15 min) over the motor cortex with the coil always in the optimal orientation. MEPs were evoked by both monophasic and biphasic stimuli. Results MEPs were initially significantly reduced after monophasic but not biphasic rTMS. However, a late reduction was seen after biphasic rTMS. Limitations These motor cortical findings may not be directly applicable to prefrontal rTMS. Conclusions This study confirms that low frequency rTMS with monophasic pulses produces more corticospinal inhibition than with biphasic pulses, even when the direction of current and intensity are as well-matched as possible.