Prolagus is the most important lagomorph genus of European Cenozoic. Its systematics is mainly based on dental characters that show great inter- and intraspecific variability: this often leads non-specialists to incorrect systematic attributions, with all the consequent applicative problems that this implies. Aim of this paper was to test a specific Fourier Analysis, Complex Discrete Fourier Transform (CDFT), to aid Prolagus systematics. To verify the efficacy of Fourier Analysis applied to Prolagus systematics, empirical tests have been performed on P/3 anteroconid contour of the well-known species P. tobieni, P. oeningensis, P. sorbinii, P. michauxi, P. italicus and P. sardus. At the specific level, a correspondence between most Fourier Analysis results and available phylogenetic data is evident (the clear separation of P. tobieni from all other species, the clustering of the related species P. oeningensis, P. sorbinii and P. michauxi). In other cases, the discrepancy between Fourier Analysis outputs and phylogenetic data (as in the case of P. italicus, resulted more closely related to P. sardus than to its ancestor P. sorbinii), instead of a limitation of the method, may be read as a hint for further research lines. At the population level, the results fitted and implemented those of classic morphodimensional analyses. These encouraging results led to apply Fourier Analysis to obtain additional hints about the systematic position of some extremely scanty Messinian to earliest Pleistocene Prolagus remains from the Italian, Balkan and Anatolian peninsula. As for Messinian Prolagus specimens, their systematic attributions to P. sorbinii and P. michauxi were confirmed. Pliocene specimens from Greece and Anatolia resulted similar to P. sorbinii and P. italicus and not to P. michauxi as suggested in the literature. As for an earliest Pleistocene Italian not yet specifically determined remain, a close similarity to P. sorbinii, never previously suggested, was evidenced. Fourier Analysis proved to be a valid methodology (complementary to existing morphodimensional analyses) to be applied in Prolagus systematics at different systematic levels.