The study included 142 patients (87 women, 55 men) (mean age 36.2 +/- 8.3 yr) after ischemic stroke caused by dissection of cerebral arteries (D) (n = 37), anti-phospholipid syndrome (APS) (n = 55) or cardiogenic embolism (CE) (n = 11). Stroke of unknown origin (cryptogenic) was diagnosed in 39 patients. Mutations of 5,10-methylenetetrahydropholate reductase (MTGPR), prothrombin, and coagulation factor V genes were documented by PCR in 38, 0, 3% of D cases, 55.9, 9, 13% of APS cases, 73, 9, 0 CE cases, 57, 5, 0% of cases with cryptogenic stroke compared with 43, 0, 0% in controls. Mutations in MTGPR gene in CE cases, prothrombin gene in APS and CE cases, coagulation factor V gene in APS cases occurred more frequently than in control (p < 0.05). They, were more frequent in APS/CE than in D (p < 0.05). Mutation rate in cryptogenic stroke was not significantly different from that in control (p < 0.05). It is concluded that the above mutations are not involved in pathogenesis of cryptogenic stroke, whereas those of prothrombin and coagulation factor V genes may enhance the thrombogenic potential in APS and CE patients. The role of MTGPR gene mutation in pathogenesis of cardiogenic stroke needs clarification.