AbstractBackground and PurposeGray matter (GM) volumes have previously shown variations in different regions in patients with migraine, particularly in cortical regions. This study focused on comparative volumetric assessment of deep brain structures, including GM and cerebrospinal fluid (CSF), in patients with and without migraine. Furthermore, a relationship between the measured volumes and clinical features of migraine was investigated.MethodsIn a cross‐sectional study, 30 patients with episodic migraine and 30 subjects without migraine were investigated through brain MRI. The migraine group had a mean ± standard deviation (SD) age of 39 ± 12 (77% female, 23% male), and the control group had a mean ± SD age of 40.5 ± 11 (70% female, 30% male). Groups were matched in terms of age, gender, and comorbidities. T1‐weighted images were transferred to an automated MRI analysis tool to measure the volumes of interested regions.ResultsOur results showed that GM volumes of caudate nuclei, thalami, mammillary bodies, right nucleus accumbens, and CSF volumes of lateral ventricles in migraine group were significantly higher compared to the control group. In addition, migraine was independently associated with a higher volume of caudates, thalami, mammillary bodies, and lateral ventricles but a lower volume of the third and fourth ventricles. An analysis of migraine clinical features revealed that a longer duration of migraine was associated with a lower GM volume of the right mammillary body and higher CSF volumes of lateral ventricles, and the third ventricle.ConclusionOur study supported the hypothesis that migraine is independently associated with the volumes of deep brain structures, specifically the thalamus, caudate, mammillary body, and ventricular system.