Brain magnetic resonance imaging (MRI) studies in migraine patients have demonstrated lesions consisting of focal regions of increased signal intensity within the white matter. Antiphospholipid antibodies are known to have a role in many diseases including migraine. The aim of the present study was to ascertain the relationship between MRI-visualized cerebral focal hyperintense lesions and serum antiphospholipid antibody levels, as well as blood coagulation parameters in migraine patients. One hundred and two (77 females, 25 males, mean age 33.8 ± 11.1) consecutive migraine patients and a control group of 94 (70 females, 24 males, mean age 33.2 ± 10.8) healthy subjects were enrolled. All individuals underwent brain MRI. Complete blood examinations, autoantibodies, antiphospholipids antibodies including anticardiolipin and lupus anticoagulant (aCL, LAC), antithrombin III, Protein C and S serum levels were ascertained in the subjects who presented white matter lesions on MRI. Twenty-seven (26.4%) migraine patients and six (6.3%) healthy subjects in the control group showed focal regions of increased intensity signal within cerebral white matter (odds ratio 5.3, 95% CI: 1.98–16.36). In migraine patients with white matter lesions, antiphospholipid antibodies were not detected and serum levels of antithrombin III, and proteins C and S were normal. White matter lesions in migraine patients are fairly common. This finding is not associated with antiphospholipid antibodies or abnormal coagulation parameters. The significance of such lesions at present remains unclear.