Abstract We propose for the first time a direct comparison between brain and endocast characteristics—the number, position, length and proportion of sulci as revealed by the evidence on the brain and their corresponding marks on the endocast that is the internal surface of the skull—in the same living individuals. Using a tailored MRI imaging methodology developed to overcome the limitations inherent to medical imaging on healthy subjects, we compare 3D models of the brain and of the endocast obtained from the same cohort of 75 volunteers. These data were quantified in terms of observation frequency, proportion of dimension for the same structures on the endocast compared to the brain and variation among the analysed sample. We show that identifiable marks on the endocast are often short, discontinuous, and primarily located in the lower regions (particularly in the inferior frontal and temporal lobes areas). This observation contradicts previous practices of drawing long, straight marks on fossil endocasts. An unexpected result of the study is the discovery of endocranial marks unrelated to cerebral sulci, called MNAS (for endocranial Marks Not Associated with Sulci). These marks represent approximately 12% of the depressions observed and pose a challenge for the interpretation of fossil endocasts. Finally, we propose with this work a new standardised approach to studying fossil endocasts, which combines precise guidelines for sulci variation description as well as for inter‐individual comparisons, and cross‐validation by several researchers. The development of a new approach based on a large quantity of anatomical information presented in the present study, offers new perspectives for reconstructing the anatomy of fossil hominin's brain in a more objective framework, and will have a lasting impact for the study of the evolution of the hominin brain, particularly functional lateralisation and cognitive abilities.