A startling auditory stimulus delivered during preparation for execution of a ballistic movement in a simple reaction time task experiment induces two effects: a startle response and a reaction time shortening (the StartReact effect). We investigated whether prepulse inhibition of the startle response is effective in suppressing either one of these effects during motor preparation. Twelve healthy volunteers were presented with seven different experimental conditions in random order: while at rest, subjects received a low intensity electrical shock on the middle finger of the left hand (Prep), a loud auditory stimulus (Start), or a combination of these two (PrepStart). While engaged in preparation for a visual simple reaction time task, they were presented with the imperative signal for execution of the reaction (React), or with any of the combinations PrepReact, StartReact, or PrepStartReact. We recorded the EMG activity from the orbicularis oculi and the sternocleidomastoid muscles to assess the startle response, and from the wrist extensor muscles to assess reaction time. The startle response was markedly reduced when Prep was presented 100 ms before Start regardless of whether the subjects were at rest or preparing for the reaction. Reaction time shortened significantly in StartReact trials with respect to React trials, and the percentage shortening was not different in trials in which Prep preceded StartReact and inhibited the startle response. The fact that prepulse inhibition of the startle response is not accompanied by modification of the StartReact effect indicates that there are separate physiological mechanisms for the two effects, an observation that has implications for further understanding of the processes underlying motor preparation for a ballistic reaction.