To investigate whether the early effects of voluntary teeth clenching (VTC) among the first dorsal interosseous (FDI), abductor digiti minimi (ADM), and abductor pollicis brevis (APB) muscles are differently modulated depending on their muscle properties, we examined the responses of motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation with selected current directions and by brainstem magnetic stimulation (BMS). Although MEP responses with anterior-medially current direction (preferentially elicited I1-waves) were facilitated in all three muscles, those responses with posterior-laterally current direction (preferentially elicited I3-waves) were different among FDI, ADM, and APB muscles. That is, MEP responses in FDI and APB muscles were significantly reduced, whereas those responses in ADM muscle were not significantly reduced. Further, inhibitory effects of VTC in FDI muscle were more potent than those in ADM or APB muscles. On the other hand, the responses to BMS were unchanged by VTC in all three muscles, suggesting that the modulations of MEP were attributed to the cortical origin. On the basis of our previous findings that the inhibitory connections in FDI muscle are more potent than those in ADM muscle (Takahashi et al. in Clin Neurophysiol 116:2757-2764, 2005), the cortical effects of VTC among three hand muscles are differently modulated, depending on muscle properties, presumably the extents of inhibitory connections to corticospinal tract neurons. Considering that the functional capacity in FDI muscle is higher than that in ADM or APB muscles, the cortical inhibitory effect of VTC might contribute to the sophisticated regulation of the motor outputs even during VTC.