Our aim was to determine whether ventilation and swallowing tasks can modify oropharyngeal cortical motor organisation. Mylohyoid motor-evoked potentials (MEP) induced by non-focal (NF) and focal (F) magnetic stimulations were recorded in nine healthy volunteers four times, with 1 week between each recording. Baseline values were evaluated and their reproducibility was assessed 1 week later. Thereafter, the subjects were asked to perform swallowing and ventilation tasks in random order 15 min per day for 1 week. The NF MEP amplitudes after the swallowing and ventilation tasks increased after effortful swallows (p<0.001) and ventilation efforts (p<0.001). The F MEP amplitudes obtained after focal cortical stimulations increased after effortful swallows (p<0.01) and ventilation efforts (p<0.05). The cortical magnitude of the oropharyngeal muscle representation increased after swallowing practice (p<0.01). In conclusion, swallowing and ventilation tasks modified the motor cortex of oropharyngeal muscles and should be evaluated for use in rehabilitation strategies.