An automated system for tool mark analysis includes an acquisition mechanism for acquiring 3D data of tool marks left on the surfaces of specimens by tools, a signature generation module for generating tool mark signatures from the acquired data, an analysis unit for comparing pairs of the tool mark signatures to obtain a numerical similarity value reflective of their similarity, and a database in which the similarity values are stored. An automated method for tool mark analysis involves the steps of acquiring the 3D data of tool marks, generating the tool mark signature, statistically evaluating pairs of the tool mark signatures, and providing a numerical similarity value for each pair of tool mark signatures reflecting the degree of similarity between the tool mark signatures of each pair. The method is carried out with automated assistance of a computer.