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Inhibition is a central component of human behavior. It enables flexible and adaptive behavior by suppressing prepotent motor responses. In former studies, it has been shown that sport athletes acting in dynamic environments exhibit superior motor inhibitory control based on sensory stimuli. So far, existing studies have corroborated this in manual motor response settings only. Therefore, this study addresses the effector specificity of the inhibition benefit in elite athletes compared to physically active controls. A sport-unspecific stop-signal task has been adapted for hand as well as feet usage and 30 elite handball players as well as 30 controls were tested. A repeated-measures ANOVA with the two factors “effector” (hands, feet) and “group” (expert, recreational athletes) was conducted. Our results suggest no group differences in two-choice response times, but a convincing superiority of handball players in inhibitory control (i.e., shorter stop-signal reaction times), predominantly when responding with their hands, with weaker differential effects when responding with their feet. This suggests that motor inhibition might be a comprehensive performance characteristic of sport athletes acting in dynamic environments, detectable predominantly in eye-hand coordination tasks.