Low-frequency repetitive transcranial magnetic stimulation (rTMS) of the primary motor cortex (M1) results in a lasting decrease of motor evoked potentials (MEPs). Here we investigated the effects of supra-threshold rTMS (15 min, 1 Hz) to the left M1 on the excitability of the stimulated and homologous (unstimulated) M1 in healthy subjects by using single and double pulse TMS before and after rTMS. We found reduction of MEP amplitudes on the stimulated side and, most importantly, disinhibition of intracortical excitability of the homologous M1. This crossed effect of rTMS supports the concept of a physiological balance of reciprocal inhibitory projections and emphasizes that rTMS can induce remote effects that are relevant for the physiological interpretation of such interventions.