Locked-in syndrome is a dramatic clinical condition, the patient is awake, can listen and breath, but is unable to move any muscle, conserving only the vertical eye movements. The most common cause of locked-in syndrome is the thrombosis of the basilar artery and commonly leads to death, frequently due to pneumonia. Intravenous and intra arterial thrombolysis have been used successfully in a selective group of patients with ischemic stroke. There is only one report of two patients with locked-in syndrome who were treated successfully with intra arterial thrombolysis. Other authors, based in their experiences, do not recommend this treatment. We report two female patients aged 63 and 26 years, with Locked-in syndrome due to a basilar thrombosis who were treated successfully with intra arterial thrombolysis using recombinant tissue plasminogen activator (r-TPA). The lapses between the onset of the symptoms and thrombolysis were 5 and 8 hours respectively. A complete recanalization was obtained in both patients during the thrombolysis. One year after, the first patient has only a moderate ataxia, walking with assistance and the other has a normal neurological examination.