The recent application of microtomographic techniques to dental morphological studies has revealed an untapped source of biological information about extinct and extant human populations. In particular, this methodology has helped to characterize internal dental structures (enamel–dentine junction, pulp chamber, and radicular canals), maximizing the amount of information that can be extracted from a given specimen. In this study, we present a three-dimensional evaluation of the dental roots of the Sima del Elefante mandible, ATE9-1 (Atapuerca, Spain) by visual inspection, and by tomographic and microtomographic techniques. With 1.3 Myrs of age, this fossil represents the earliest hominin remains in Europe, and one of the very few human fossils for this period and region. Through this case study we aim to present a protocol for the description of the internal dental spaces, exemplify how the application of microtomographic techniques can significantly increase the amount of relevant and informative morphological features (even in the case of fragmentary/heavily worn teeth or teeth with hypercementosis), and explore some biological considerations about external and internal root morphology. There is neither a general nor straightforward correspondence between the external root morphology and the root canals. In cases where a high degree of hypercementosis is present, the external root anatomy can be highly confusing. Indeed the assessment of the internal root anatomy of ATE9-1 teeth has led us to the reclassification of the LC and the LP3 with respect to previous publications. The results of this study suggest that internal root anatomy could be used as a complementary source of biological information.