The sand pit of Pécs-Danitzpuszta is one of the most important mixed Neogene vertebrate localities in Hungary, with older Miocene (Langhian – Serravallian) terrestrial and marine animal remains re-deposited into the upper Miocene (Tortonian) Lake Pannon sediments. Due to the mixed status of the Pécs-Danitzpuszta vertebrate assemblages, limited information is available about the former depositional environment and age of these fossils. However, the rare earth element (REE) composition of the fossil apatite can help to determine the stratigraphic origin and the early depositional environments of unprovenanced vertebrate remains. In this study, the REE composition of more than 60 vertebrate fossils, among them reworked and in situ remains from the Mecsek Mountain, were analysed. The results allowed separation between the Badenian, Sarmatian, and Pannonian aged fossils. The REE content and their distribution also helped us characterise the ancient depositional conditions of the investigated reworked fossils. Furthermore, several different types of vertebrate fossils were analysed, resulting in a large database that helped clarify the likely timings and mechanisms of REE uptake at this locality. Apparent variation in REE chemistry within bones (cortical vs cancellous) and teeth (enamel vs dentine) are best linked to fractionation along the REE series during their incorporation.