Purpose One out of three migraine patients might have accompanying restless legs syndrome (RLS). In our study, we aimed to compare the volumes of the brain structures of migraineurs with and without RLS. Methods We had 37 female patients with migraine and 17 females as the control group. Nineteen migraineurs had no RLS (RLS0) and 18 migraineurs had comorbidity of RLS (RLS1). The volumes of the brain structures were obtained by manual measurements, volBrain, and voxel-based morphometry (VBM). Manually, we measured caudate and putamen volumes. We used age, years of education, depression, anxiety scores, and total intracranial volume as covariates. Results According to VBM analyses, the volumes of the left superior occipital gyrus and precuneus were increased, and the substantia nigra and cuneus were decreased in the RLS1 group compared with the RLS0 group. RLS1 patients had larger superior temporal gyrus, Brodmann area 38, and left insula, and RLS0 patients had larger Brodmann area 22, right superior temporal gyrus, and Heschl gyrus compared with controls. Migraine and RLS0 patients had a smaller corpus callosum anteriorly, whereas RLS1 patients had a smaller splenium. Caudate volumes were larger in migraine patients via the three techniques. There was a positive relation between the caudate and putamen volumes and attack frequency. Conclusions Comorbidity of RLS might be a confounding factor in structural neuroimaging studies in migraine. Deficits in the visual network seem to be related to accompanying RLS; deficits in the auditory network are particularly related to migraine.