Palaeoecological and biostratigraphical interpretations have been traditionally based on the presence in the fossil record of certain species. Nevertheless, there are many taphonomic factors controlling the species composition and their relative abundance in a fossil site that may alter spatial and temporal correlations between the site where fossils have been found and the place where past beings were living. Taphonomic studies have been conducted at different sites from Atapuerca-Ibeas cave complex. This cave complex (in Burgos, Spain) includes several karstic sites with extensive evidence of human activity and a complete record of vertebrate remains of the middle Pleistocene, as well as abundant human fossils. The small mammal taphonomic analysis of one of these sites (Penal) is explained and discussed here in detail to show the taphonomic procedure. Stratigraphical correlation between levels at the Penal site is particularly difficult and correlations have been proposed here based on taphonomic data. Since 1980 a working hypothesis suggested a sedimentary connection between Penal and another site named Dolina, presently separated by an abandoned railway cutting. In order to test this hypothesis, the results of Penal obtained from the present study are compared to previous analysis done in Dolina. It is also attempted here through taphonomic comparison of these two sites to obtain a better understanding of the past context where hominids inhabited.