In this document we describe our method and the results obtained for comparing jaws of prehistoric humans. Our main goal was twofold: (1) establish a methodology for comparing the structure of 3D shapes of scans of jaws using geometric data analysis techniques, and (2) use this methodology for comparing and clustering individual objects according to their geometric similarity. Moreover, we also applied geometric modeling techniques to establish a “clean” version of the dataset, without significant artefacts present in the original data, such as large missing parts. We then applied our analysis techniques both on the original and the clean dataset in order to validate our comparison results. For our core task of shape comparison, we used recent state-of-the-art shape matching methods and we present similarity results using different comparison metrics.