We investigated whether input/output curves of human motor cortex could provide similar information to cortical mapping under two conditions where the motor maps are known to change dramatically: ischaemic anaesthesia and amputation. Stimulus/response curves were constructed by recording the size of EMG responses evoked in arm muscles with transcranial magnetic stimulation at a single site using a range of intensities. Changes in the slope of this relationship during ischaemic anaesthesia (6 normal subjects) or amputation (two patients) were compared to changes in cortical motor maps produced by stimulating different sites at the same intensity. At rest both interventions increased map areas, as well as the slope of the stimulus/response curves. During voluntary activity they had no effect. We conclude that stimulus/response curves can detect changes in cortical motor maps, and discuss potential mechanisms for this effect.