Type 2 diabetes and stroke are associated with reduced brain volumes and independently present a high risk for cognitive impairment or dementia. The interaction between diabetes and stroke and its effects on brain atrophy are unknown. We used linear mixed-effect modelling to estimate rates of atrophy over two years based on FreeSurfer segmentation of MR images of healthy participants and patients with type 2 diabetes and/or stroke. Cerebral atrophy, defined by volume reductions in specific regions of interest, was accelerated the most in the group with only type 2 diabetes. Thalamus was affected more by stroke.