Flexible behavior requires the ability to delay a response until it is appropriate. This can be achieved by holding either a sensory or a motor representation on-line. Here we assess whether maintenance of sensory or motor material drives the motor system to different functional states, as indexed by alterations of corticospinal excitability. We used single-pulse TMS to measure cortico-spinal excitability evoked during the delay period of a novel paradigm in which task contingencies, rather than explicit verbal instructions, induced participants to use either sensory or motor codes to solve a delay-non-match-to-sample (DNMS) task (Toni et al. 2002b). This approach allowed us to probe the state of the motor system while the participants were retaining either sensory or motor codes to cross the delay period, rather than the control of short-term storage driven by verbal instructions. When participants could prepare the movement in advance (PREPARATION trials), the excitability of the motor cortex contralateral to the moving hand increased, while the excitability of the ipsilateral motor cortex decreased. The increase in excitability was confined to the prime mover, whereas the decrease in excitability extended to cortical territories controlling muscles unrelated to the response. Crucially, these changes in excitability were evoked only during PREPARATION trials, but not during trials in which subjects needed to maintain sensory items on-line (MEMORY trials). We infer that short-term storage of sensory information and preparation of motor responses have differential and specific access to the output stage of the motor system.