Objective: Type 2 diabetes mellitus (T2DM) is associated with cortical atrophy on MRI. It is unclear whether this atrophy is global or if there are areas with particular vulnerability. We compared regional cortical atrophy between patients with T2DM and controls and examined determinants of atrophy within the T2DM group. Methods: Cortical surface, volume and thickness were compared between 56 patients with T2DM and 30 controls, both globally and regionally, using the Freesurfer software package. The relationship between atrophy and HbA1c levels, diabetes duration, hypertension, a history of macrovascular disease and cerebral small vessel disease was analyzed within the T2DM group, with linear regression analyses, adjusted for age and gender. Results: Total cortical surface, total cortical volume and mean cortical thickness for both hemispheres were consistently lower in the T2DM group (between group differences: 0.5-4%), but the effects were only significant in the right hemisphere (p < 0.05). Post-hoc regional analyses revealed significant differences in the hippocampal region (between group differences cortical thickness and volume: 5-20.5%) and the middle temporal gyrus (between group differences cortical surface and volume ~ 8%). Within the T2DM group, smaller cortical thickness of the hippocampal region was associated with cerebral small vessel disease, but no associations between vascular or metabolic determinants and cortical atrophy were found. Conclusion: The effects of T2DM on cortical grey matter are most pronounced in the temporal lobe. This should be considered when atrophy is used as a marker in etiological or therapeutical studies.