We have investigated the prevalence and possible association of inherited prothrombotic risk factors in patients with primary Raynaud's phenomenon (PRP) and migraine. We performed genotypic analysis of FVLeiden, prothrombin G20210A, methyltetrahydrofolate reductase C677T and FXIII-A V34L mutations in these patients. Two hundred patients with primary Raynaud's phenomenon of Hungarian origin with migraine (57 female, one male, mean age of 43.8 ± 11.5 years) or without migraine (101 female, 41 male, mean age of 41.8 ± 14.5 years) were included in this study. Duration of PRP among migrainous patients was significantly longer than patients without migraine. The prevalence of methyltetrahydrofolate reductase T677 allele among patients with migraine was significantly higher than in patients without migraine (odds ratio 2.1, 95% CI: 1.4-3.3, p = 0.001). The prevalence of other thrombosis-associated alleles did not differ between patients with or without migraine. FVLeiden mutation, prothrombin G20210A mutation, and FXIII-A V34L polymorphism have no apparent effect on the occurrence of migraine in PRP.