The TT genotype of a functional factor XII (FXII) C46T gene polymorphism was shown to be a risk factor for peripheral venous thrombosis. We tested whether this genetic variant also increases the risk for cerebral venous thrombosis (CVT).We performed a case-control study including 78 consecutive patients with proven CVT and 201 healthy population controls from South Germany. The FXII C46T genotype was assessed using a PCR technique.The TT genotype of the FXII C46T polymorphism was more common in patients (16.7%) than in controls (5.5%). A strong association of the TT genotype with CVT was found, which was independent of covariables (adjusted odds ratio 4.57; 95% CI 1.55 to 13.41; p = 0.006).The TT genotype of the functional factor XII C46T gene polymorphism may be a new independent risk factor for cerebral venous thrombosis (CVT). Our finding warrants confirmation in an independent study before this genetic variant should be added to the panel of established risk factors for CVT.