Humans can be classified as early, intermediate and late chronotypes based on the preferred sleep and wakefulness patterns. The anatomical basis of these distinctions remains largely unexplored. Using magnetic resonance imaging data from 113 healthy young adults (71 females), we aimed to replicate cortical thickness and grey matter volume chronotype differences reported earlier in the literature using a greater sample size, as well as to explore the volumetric white matter variation linked to contrasting circadian phenotypes. Instead of comparing the chronotypes, we correlated the individual chronotype scores with their morphometric brain measures. The results revealed one cluster in the left fusiform and entorhinal gyri showing increased cortical thickness with increasing preference for eveningness, potentially providing an anatomical substrate for chronotype-sensitive affective processing. No significant results were found for grey and white matter volume. We failed to replicate cortical thickness and volumetric grey matter distinctions in the brain regions reported in the literature. Furthermore, we found no association between white matter volume and chronotype. Thus, while this study confirms that circadian preference is associated with specific structural substrates, it adds to the growing concerns that reliable and replicable neuroimaging research requires datasets much larger than those commonly used.