BACKGROUND Repetitive transcranial magnetic stimulation (rTMS) is a simple and non-invasive method of augmenting motor recovery after stroke, probably mediated by restoring inter-hemispheric activation balance. This placebo-controlled pilot study examined the possible benefit of stimulating the lesioned hemisphere (5-Hz rTMS) or inhibiting the contra-lesional hemisphere (1-Hz rTMS) on clinical recovery of motor function in patients with ischaemic stroke and assessed the sustainability of the response. METHODS Sixty patients with ischaemic stroke (>1 month from onset) with mild-to-moderate hemiparesis were randomized to receive 10 daily sessions of either sham rTMS, 5-Hz ipsi-lesional rTMS or 1-Hz contra-lesional rTMS, in addition to a standard physical therapy protocol. Serial assessments were made over a period of 12 weeks by the thumb-index finger tapping test (FT), Activity Index (AI) score and the modified Rankin Scale (mRS). RESULTS In contrast to control patients, those receiving active rTMS as ipsi-lesional 5-Hz stimulation or 1-Hz contra-lesional stimulation showed statistically significant improvement on the FT test, AI scores and mRS score at 2 weeks, and the effect was sustained over the 12-week observation period. No significant adverse events were observed during treatment in either group. CONCLUSIONS Repetitive TMS has beneficial effects on motor recovery that can be translated to clinically meaningful improvement in disability in patients with post-stroke hemiparesis, with a well-sustained effect. The similarity of inhibitory and stimulatory rTMS in producing these effects supports the inter-hemispheric balance hypothesis and encourages further research into their use in long-term neurorehabilitation programmes of patients with stroke.