Paired-pulse transcranial magnetic stimulation (TMS) at short interstimulus intervals was employed to investigate short-term effects of 5-Hz repetitive TMS (rTMS) over the primary motor hand area (M1(HAND)) on intracortical excitability. In ten healthy individuals, 1250 pulses of 5-Hz rTMS were applied at 90% of motor resting threshold over the left M1(HAND). Ten minutes after 5-Hz rTMS, paired-pulse inhibition was significantly reduced, whereas paired-pulse facilitation was not modified. Sham-rTMS had no lasting effect on intracortical excitability. These findings suggest that subthreshold 5-Hz rTMS causes a short-term modulation of the excitability of intracortical circuitry in the stimulated M1(HAND). The lasting effect of subthreshold 5-Hz rTMS on intracortical inhibition provides a useful probe for studying short-term plasticity of the human M1(HAND).