Several experimental protocols induce lasting changes in the excitability of motor cortex. Some involve direct cortical stimulation, others activate the somatosensory system and some combine motor and sensory stimulation. The effects usually are measured as changes in amplitude of the motor-evoked potential (MEP) or short-interval intracortical inhibition (SICI) elicited by a single or paired pulses of transcranial magnetic stimulation (TMS). Recent work has also tested sensorimotor organisation within the motor cortex by recording MEPs and SICI during short periods of vibration applied to single intrinsic hand muscles. This sensorimotor organisation is focal: MEPs increase and SICI decreases in the vibrated muscle, whilst the opposite occurs in neighbouring muscles [1]. In six volunteers we compared the after effects of three protocols that led to lasting changes in cortical excitability: (i) paired associative stimulation (PAS) between a TMS pulse and an electrical stimulus to the median nerve; (ii) sensory input produced by semi-continuous muscle vibration of the abductor pollicis brevis (APB); and (iii) motor practice of rapid thumb abduction, on MEPs and SICI at rest and on the sensorimotor organisation. PAS increased MEP amplitudes at rest (143±5%), but had no effect on either SICI at rest or on sensorimotor organisation. The vibration intervention had no effect on MEPs or SICI at rest, but changed the sensorimotor organisation in terms of expanding the facilitatory effect of subsequent APB vibration on neighbouring muscles. Motor practise had a dual effect and increased MEPs at rest (139±7%), as well as affecting sensorimotor organisation similar to the vibration intervention. The implication is that different protocols target different sets of cortical circuits. We speculate that protocols that involve repeated activation of motor cortical output lead to lasting changes in the efficacy of synaptic connections in output circuits, whereas protocols that emphasise sensory inputs affect the strength of sensory inputs and the way they influence motor circuits.