Microscopy, mass spectrometry and X-ray diffraction methods were used to analyse 415 samples of natural and archaeological flint from Sierra de Atapuerca (Burgos, Spain) in order to define the different types from Neogene and Cretaceous formations in the study area, infer their genetic context and ascertain the supply sources used by hunter-gatherers who exploited this area in the Upper Pleistocene. A statistical classification model was also designed using linear discriminatory analysis and support vector machines which permitted the differentiation of the flint on an age basis.