Objective To investigate the effect of thrombin on periventricular tissue. Methods Thrombin solution (10U/10μl) was infused into the ventricles of rats. Then, the local cerebral blood flow (rCBF) and blood-brain barrier (BBB) permeability in the area of basal ganglia and thalamus were measured. In separate experiments neurons were cultured in the medium with thrombin, and lactate dehydrogenase was determined. Results The thrombin induced blood-brain barrier disruption and neuron death in the culture, whereas cerebral blood flow did not drop to the injury level. Conclusion Periventricular tissue damage suffering from the thrombin and blood-brain barrier disruption and cell toxicity could elicit pathological mechanisms.