Behavioral studies have shown that humans account for inertial acceleration in their decisions of hand choice when reaching during body motion. Physiologically, it is unclear at what stage of movement preparation information about body motion is integrated in the process of hand selection. Here, we addressed this question by applying transcranial magnetic stimulation over motor cortex (M1) of human participants who performed a preferential reach task while they were sinusoidally translated on a linear motion platform. If M1 only represents a read-out of the final hand choice, we expect the body motion not to affect the MEP amplitude. If body motion biases the hand selection process prior to target onset, we expect corticospinal excitability to modulate with the phase of the motion, with larger MEP amplitudes for phases that show a bias to using the right hand. Behavioral results replicate our earlier findings of a sinusoidal modulation of hand choice bias with motion phase. MEP amplitudes also show a sinusoidal modulation with motion phase, suggesting that body motion influences corticospinal excitability which may ultimately reflect changes of hand preference. The modulation being present prior to target onset suggests that competition between hands is represented throughout the corticospinal tract. Its phase relationship with the motion profile suggests that other processes after target onset take up time until the hand selection process has been completely resolved, and the reach is initiated. We conclude that the corticospinal correlates of hand preference are modulated by body motion.