Thrombophilia is frequently associated with venous thromboembolism (VTE) including cerebral venous sinus thrombosis (CVST). The possibility of thrombophilia was examined in 12 patients with CSVT diagnosed in the past 9 years. Thrombophilia due to abnormalities in antithrombin (AT), protein C (PC), or protein S (PS) or antiphospholipid syndrome (APS) was evaluated. Nine patients with abnormally decreased AT, PC or PS and one patient with APS were examined. Of the nine patients examined by a gene analysis of AT, PC, or PS, one had a congenital AT deficiency, one had a congenital PC deficiency, and two had congenital PS deficiencies including a novel mutant (Gly189Ala). AT, PC and PS levels were all decreased in one patient, PS level was decreased in three patients, and AT level was decreased in one patient at the onset of CVST, but these concentrations improved after treatment. CVST is frequently associated with thrombophilia and a transient decrease in AT, PC or PS may be a causal factor.