The prognosis of vertebrobasilar occlusion is grave and therapeutic options are limited. The aim of the present study was to develop a new model of embolic hindbrain ischemia in the rat that closely resembles the clinical situation and that can be used to study pathophysiology and treatment options. After thoracotomy in 20 male Wistar rats, 15 animals received an injection of in vitro prepared autologous blood clots into the left vertebral artery. Five animals without clot injection served as controls. Neurological deficits were assessed in all animals 2 h after embolism. After 2 h, five animals were sacrificed to measure cerebral blood flow (CBF) by iodo-antipyridine autoradiography, and to calculate early cerebellar swelling by comparison of both hemispheres in brain slices. In these animals, autoradiography revealed ipsilesional brain swelling and significantly reduced blood flow values relative to the contralateral (unaffected) structures. Immunohistology showed the typical pattern of focal cerebral ischemia in the brain stem and/or cerebellum in 7 of 10 animals allowed to recover to 24 h. Hence, successful thromboembolism was achieved in 12 of 15 animals (80%). With this novel model, the pathophysiology and potential treatments of posterior circulation stroke can be investigated.