Case series have demonstrated an increased incidence of white matter lesions (WMLs) in patients with migraine. It is controversial whether the evidence of subclinical brain lesions relates to a higher risk of cerebrovascular disease. The objective of this study was to evaluate the association between magnetic resonance imaging (MRI) subclinical brain lesions and cerebrovascular risk factors (hyperhomocysteinaemia, MTHFR genotype, patent foramen ovale, hypertension, smoking and hypercholesterolaemia). From our database of 1201 patients followed at our Headache Clinic since September 2003 we analysed the MRI findings of 253 individuals. All MRI were blindly analysed by a second neuroradiologist (C.A.) and patients with WMLs (study group) were evaluated. In order to assess the association of WMLs with specific vascular risk factors, patients with WMLs were matched, according to age, sex and ICHD II diagnosis, with an equal number of individuals with normal MRI (control group). Headache was classified by the International Classification of Headache Disorders (ICHD 2004) criteria. We did not find any statistically significant difference between the two groups with regard to the presence of the cerebrovascular disease risk factors considered. Our results confirm that the WMLs are not related to the cerebrovascular disease risk factors.