Based on previous clinic-based MRI studies showing regional differences in the cerebral cortex between those with and without headache, we hypothesized that headache sufferers have a decrease in volume, thickness or surface area in anterior cingulate cortex (ACC), prefrontal cortex (PFC), and insula. In addition, exploratory analyses on volume, thickness and surface area across the cerebral cortical mantle were performed. 1006 participants (50-66 years) from the general population were selected to an imaging study of the head at 1.5 T (HUNT-MRI). 283 individuals suffered from headache, 80 with migraine and 87 with tension-type headache, whereas 309 individuals did not suffer from headache and were used as controls. T1 weighted 3D scans of the brain were analysed with voxel-based morphometry and FreeSurfer. The association between cortical volume, thickness and surface area and questionnaire-based headache diagnoses was evaluated, taking into consideration evolution of headache and frequency of attacks. There were no significant differences in cortical volume, thickness or surface area between headache sufferers and non-sufferers in ACC, PFC or insula. Similarly, the exploratory analyses across the cortical mantle demonstrated no significant differences in volume, thickness or surface area between any of the headache groups and the non-sufferers. Maps of effect sizes showed small differences in the cortical measures between headache sufferers and non-sufferers. Hence, there are probably no or only very small differences in volume, thickness or surface area of the cerebral cortex between those with and without headache in the general population.