The palaeontological collections of the museum consist mainly of Early Palaeozoic fossils from Estonia
. The most numerous among these are fossils of Ordovician and Silurian marine invertebrates - brachiopods, trilobites, gastropods, corals, bryozoans, echinoderms, graptolites and eurypterides. The collections also include the fossils of early vertebrates: jawless and jawed fishes. The oldest palaeontological and lithological materials of the museum are dated from the middle of the 19th century. The museum houses the collections of several famous researchers of Estonian geology, such as academician Fr. Schmidt, E. v. Koken and A. v. Pahlen. The collections of the museum contain several published type specimens found in the second half of the 19th century and first half of the 20th century, including the fossil of Bothriocidaris pahleni, one of the oldest sea urchins in the world, which was found from Haljala Stage. The palaeontological collections also contain a small amount of bone elements and skeleton fragments of Quaternary mammals, most of them originating from the northern areas of Russia
. Very few bone finds originate from the territory of Estonia
. These include two molars of the hairy mammoth (Mammuthus primigenius) found near Puurmani, which, according to the research to date, are considered to be among the youngest finds of mammoth in Northern Europe.