This collection includes information of small mammals' records obtained from the analysis of barn owl pellets. Most of the material has been collected in the region of Navarra, Spain, although other localities of the Iberian Peninsula are also included. The collection is stored in the holdings of the Museum of Zoology of the University of Navarra (MZNA) and is composed by skulls, mandibles and few skeletons of 36 species of more than 72000 georeferenced specimens. Records date from 1967 to the present covering a period of 50 years. Thus, this collection can be used in studies dealing with distribution patterns of small mammals and their changes over time which can be interesting and useful in conservation planning. The data set is available in GBIF.