Based on individual circadian cycles and associated cognitive rhythms, humans can be classified via standardised self-reports as being early (EC), late (LC) and intermediate (IC) chronotypes. Alterations in neural cortical structure underlying these chronotype differences have rarely been investigated and are the scope of this study. 16 healthy male ECs, 16 ICs and 16 LCs were measured with a 3 T MAGNETOM TIM TRIO (Siemens, Erlangen) scanner using a magnetization prepared rapid gradient echo sequence. Data were analysed by applying voxel-based morphometry (VBM) and vertex-wise cortical thickness (CTh) analysis. VBM analysis revealed that ECs showed significantly lower grey matter volumes bilateral in the lateral occipital cortex and the precuneus as compared to LCs, and in the right lingual gyrus, occipital fusiform gyrus and the occipital pole as compared to ICs. CTh findings showed lower grey matter volumes for ECs in the left anterior insula, precuneus, inferior parietal cortex, and right pars triangularis than for LCs, and in the right superior parietal gyrus than for ICs. These findings reveal that chronotype differences are associated with specific neural substrates of cortical thickness, surface areas, and folding. We conclude that this might be the basis for chronotype differences in behaviour and brain function. Furthermore, our results speak for the necessity of considering “chronotype” as a potentially modulating factor in all kinds of structural brain-imaging experiments.