Background Oropharyngeal dysphagia occurs in up to a third of patients presenting with a unilateral hemiplegic stroke, yet its neurophysiological basis remains unknown. To explore the relation between cortical motor function of swallowing and oropharyngeal dysphagia, mylohyoid, pharyngeal, and thenar electromyographic responses to stimulation of affected and unaffected hemispheres were recorded in dysphagic and non-dysphagic patients. Methods The 20 patients studied had unilateral hemispheric stroke confirmed by computed tomography. Eight of them had associated swallowing difficulties. Electromyographic responses were recorded after suprathreshold transcranial magneto-electric stimulation of affected and unaffected hemispheres with a figure-of-eight coil. Findings Stimulation of the unaffected hemisphere evoked smaller pharyngeal responses in dysphagic patients than in non-dysphagic patients (mean 64 mu V, median 48, interquartile range 44-86 vs 118 mu V, 81, 73-150) (p<0.02). With stimulation of the affected hemisphere, the pharyngeal responses were smaller than for the unaffected hemisphere but similar between the two patient groups (26 mu V, 0, 0-48 vs 54 mu V, 0, 0-80). Dysphagic and non-dysphagic patients showed similar mylohyoid and thenar responses to stimulation of the unaffected hemisphere as well as to stimulation of the affected hemisphere-unaffected mylohyoid (269 mu V, 239, 89-372 vs 239 mu V, 163, 133-307), thenar (572 mu V, 463, 175-638 vs 638 mu V, 485, 381-764); affected mylohyoid (60 mu V, 41, 0-129 vs 96 uV, 0, 0-195); thenar (259 mu V, 258, 0-538 vs 451 mu V, 206, 8-717). Interpretation The findings indicate that dysphagia after unilateral hemispheric stroke is related to the magnitude of pharyngeal motor representation in the unaffected hemisphere.