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Transcranial magnetic stimulation (TMS) of the motor cortex of one hemisphere (conditioning stimulus, CS) inhibits EMG responses evoked in distal hand muscles by a magnetic stimulus given at appropriate interval later over the opposite hemisphere (test stimulus, TS). The common interpretation attributes this effect to an inhibition produced at cortical level via a transcallosal route. The variability of cortical excitability as measured by the interhemispheric paired-pulse (PP) technique has been assessed in healthy subjects in order to compare sub- and supra-threshold intensity of CS (80% versus 120% of individual motor threshold, MT). Within- and between-subject variability relating, respectively, to interhemispheric and gender differences were also assessed. Results point to an efficacy of a magnetic CS on one hemisphere in inhibiting EMG responses of the abductor digiti minimi (ADM) stimulated by a TS delivered over the opposite hemisphere in a range of intervals centered at 12ms. These reductions were produced by the 120% suprathreshold CS, while the 80% subthreshold CS did not affect EMG responses. Females showed a higher transcallosal inhibition than males, suggesting gender differences in interhemispheric connectivity that concern the anterior half of the trunk of the corpus callosum.