The somewhat endemic condition of European mammals today in general, and thus of ungulates in particular, is a feature currently explained by fluctuating climatic conditions known from the late Pliocene to the present. All the existing ungulate families in Europe settled there during the course of the Miocene and replaced Oligocene-inherited faunas. Furthermore, the Neogene climatic deterioration played a crucial role in the decrease of ungulate diversity probably in turn setting the bases for the present depleted situation. The growing knowledge of Neogene ungulates has now become sufficient to investigate if today’s endemic situation can be traced back to the Miocene and if the endemism apparent in many mammalian faunas was randomly distributed over the European continent. A database of 695 localities spanning Europe from the early Miocene to the early Pliocene period allows a better understanding of the spatial and temporal evolution of endemism in ungulates. The results mainly point to a long and strong endemic history in southeastern Europe. The mechanisms behind this pattern may involve the particular geographic position of this area between three continents (Africa, Asia, and Europe) as well as ecological isolation through different environmental conditions prevailing there. Pliocene and Pleistocene climatic cycles probably reinforced this situation later on and were not the only processes to control what is known nowadays.