In the present work, we report that the functional serotonin transporter gene promoter (5-HTTLPR) polymorphism is involved in migraine pathogenesis. The distribution of 5-HTTLPR genotypes was significantly different in MA patients (S/S vs. S/L vs. L/L=32.7 vs. 42.3 vs. 25.0%), MO patients (18.5 vs. 39.1 vs. 42.4%) and CON (18.0 vs. 51.3 vs. 30.7%; chi-square test, p<0.05). In 5-HTTLPR S/S carriers, the odds ratio for MA risk was 2.60 (95% confidence interval [95%CI]=1.75-3.85) compared to CON, and it was 2.14 (95%CI=1.42-3.21) compared to MO. These data provide a further insight on the complex genotype-phenotype relationship involved in MA pathogenesis, and might eventually result in new and individualised prognostic and therapeutic measures.