The Vertebrate Paleontology collection comprises some 18,000 specimens from the Cambrian period (541 million years ago) and until the Quaternary period (2.6 million years ago). They are predominantly agnathans (Agnatha, jawless fish), placoderms (Placodermi, armored fish), acanthodians (Acanthodii), elasmobranchs (Elasmobranchii, sharks and rays), actinopterygians (Actinopterygii, ray-finned fish), dipnoids (Dipnoi, lung fish), and porolepiformes, osteolepiformes and coelacanths (lobe-finned fish). They mainly derive from deposits in North and East Greenland and Denmark.

The collection also houses the very important early tetrapod fossils (early four-legged vertebrates) from late Devonian deposits in East Greenland; late Triassic vertebrates from East Greenland (dinosaurs, phytosaurs, and mammals); and a large collection of ray-finned fish with some birds and turtles from the earliest Eocene marine diatomite deposits of the Limfjord area in Jutland, Denmark.