The 5HTTLPR polymorphism of the serotonin transporter gene has been associated with anxiety disorders and also migraine, suggesting a common etiological background of these disorders. This association is further supported by the high comorbidity of these disorders. In our study Spielberger's State-Trait Anxiety Inventory and the 5HTTLPR genotype were investigated in a cohort of 97 psychiatrically healthy females also including 45 migraineurs. Higher state anxiety scores were significantly associated with the s allele either in the whole sample or when the group was separated into migraineurs and non-migraineurs. Migraineurs also had a significantly higher frequency of the s allele. Our results indicate that even in a healthy population the s allele is associated with a high anxiety endophenotype. The association of migraine with anxiety may be explained by the higher rate of individuals carrying the s allele among migraineurs.