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Aim To analyse the fossil species assemblages of rodents and lagomorphs from the European Neogene in order to assess what factors control small mammal biogeography at a deep-time evolutionary time-scale.Location Western Europe: 626 fossil-bearing localities located within 31 regions and distributed among 18 successive biochronological units ranging from c . 27 Ma (million years ago; Late Oligocene) to c . 3 Ma (mid Pliocene).Methods Taxonomically homogenized pooled regional assemblages are compared using the Raup and Crick index of faunal similarity; then, the inferred similarity matrices are visualized as neighbour-joining trees and by projecting the statistically significant interregional similarities and dissimilarities onto palaeogeographical maps. The inferred biogeographical patterns are analysed and discussed in the light of known palaeogeographical and palaeoclimatic events.Results Successive time intervals with distinct biogeographical contexts are identified. Prior to c . 18 Ma (Late Oligocene and Early Miocene), a relative faunal homogeneity (high interregional connectivity) is observed all over Europe, a time when major geographical barriers and a weak climatic gradient are known. Then, from the beginning of the Middle Miocene onwards, the biogeography is marked by a significant decrease in interregional faunal affinities which matches a drastic global climatic degradation and leads, in the Late Miocene ( c . 11 Ma), to a marked latitudinal pattern of small mammal distribution. In spite of a short rehomogenization around the Miocene/Pliocene boundary (6-4 Ma), the biogeography of small mammals in the mid Pliocene ( c . 3 Ma) finally closely reflects the extant situation. Main conclusionsThe resulting biogeographical evolutionary scheme indicates that the extant endemic situation has deep historical roots corresponding to global tectonic and climatic events acting as primary drivers of long-term changes. The correlation of biogeographical events with climatic changes emphasizes the prevalent role of the climate over geography in generating heterogeneous biogeographical patterns at the continental scale.