Transcranial magnetic stimulation (TMS) is a noninvasive means of investigating the function, plasticity, and excitability of the human brain. TMS induces a brief intracranial electrical current, which produces action potentials in excitable cells. Stimulation applied over the motor cortex can be used to measure overall excitability of the corticospinal system, somatotopic representation of muscles, and subsequent plastic changes following injury. The facilitation and inhibition characteristics of the cerebral cortex can also be compared using the modulatory effect of a conditioning stimulus preceding a test stimulus. So called paired-pulse protocols have been used in humans and animals to assess GABA (gamma-amino-butyric acid)-ergic function and may have a future role directing therapeutic interventions. Indeed, repetitive magnetic stimulation, where intracranial currents are induced by repetitive stimulation higher than 1 Hz, has been shown to modulate brain responses to sensory and cognitive stimulation. Here, we summarize information gathered using TMS with patients in coma, vegetative state, and minimally conscious state. Although in the early stages of investigation, there is preliminary evidence that TMS represents a promising tool by which to elucidate the pathophysiological sequelae of impaired consciousness and potentially direct future therapeutic interventions. We will discuss the methodology of work conducted to date, as well as debate the general limitations and pitfalls of TMS studies in patients with altered states of consciousness.