The study of endocranial asymmetries of hominids is a central topic in paleoneurology. However, our knowledge about the emergence of these asymmetries during human evolution is still limited. This is partly due to the fact that, so far, these 3D asymmetries have been mostly analyzed using landmarks-based methods. Such methods are limited as they only provide a partial description of the anatomy and thus of the possible asymmetries. The endocranial anatomy may be better described by its whole contour, and the recent advent of computational tools allowing to process 3D free-form surfaces opens new tracks for automated and objective characterization of 3D endocranial asymmetries. One key problem before assessing the evolution of patterns of asymmetry in hominids is the identification of confounding factors such as age, sex and intra-specific variability. For this purpose, we use a new method for the automated quantification of 3D virtual endocranial shape of 60 Pan paniscus and 59 Pan troglodytes of different dental age and sex. 3D statistical analyzes are led to assess significantly asymmetrical areas on the endocasts within each population, and a comparison is made between the two populations. Several fossil hominin endocasts (such as Australopithecine species and fossil Homo species) are then reexamined in light of the previously estimated variability with these two extant Pan species. These new computational tools may offer a new way to address the question of how the typical endocranial asymmetries within modern humans (e.g. protrusions of the frontal and occipital lobes) emerged during evolution.