Forest management usually reduces the diversity and amount of substrates in which woodpeckers can excavate holes. In such conditions the recorded patterns of nest site selection could reflect a more reduced array of substrates than the species' nest site preferences. We analysed new data on nest sites of Middle Spotted Woodpeckers Leiopicus medius collected during 27 breeding seasons (1987–2013) in the strictly protected fragments of the Białowieża National Park in Poland. The birds could use diverse excavation substrates, of various statures, that varied in condition from living and healthy to dead and completely rotten. Middle Spotted Woodpeckers used a wide array of tree species, with little overlap in the species used in the riverine habitat (mostly Alnus glutinosa, and Fraxinus excelsior) and oak—hornbeam habitats (Carpinus betulus and Quercus robur). The birds preferred to excavate in Q. robur but avoided Tilia cordata and Picea abies. They placed holes in large trees (median girth at breast height: 202 cm), high above the ground (median 13 m), mostly in dead trees or dead fragments of living trees (66%), and often in limbs (46%). Entrances of 34% of holes were facing downwards. This pattern of hole placement differed from that found in the managed woods elsewhere, but was similar to those recorded in other old-growth forests. We suggest that Middle Spotted Woodpecker choose nest sites in places least accessible for nest predators and with a favourable microclimate.