What is the neurophysiological locus of inhibition when preparation for a manual response is countermanded? This paper evaluates data and models that pertain to inhibitory mechanisms operating in stop paradigms. In a model of De Jong, Coles and Logan (1995), (Strategies and mechanisms in nonselective and selective inhibitory motor control. Journal of Experimental Psychology: Human Perception and Performance, 21, 3, 498-511), a mechanism for nonselective inhibition operates peripheral to the motor cortex, while a selective mechanism operates at a central cortical level. We argue, however, that a peripheral mechanism of inhibition is incorrectly inferred from inhibition data available to date. Neurophysiological and psychophysiological data suggest that inhibitory processes always involve the cortex, and inhibitory effects are exerted upstream from the primary motor cortex. The prefrontal cortex and basal ganglia are candidate agents of response inhibition, whereas possible sites of inhibition are the thalamus and motor cortex.