Traditionally the dominant part of museum’s expositions and collections, as well as its scientific activities have to do with the animal world. Particular attention is paid to the biodiversity of Bulgaria and the neighbouring countries and to the description of new taxa from many countries all over the world. In the last decade considerable part of the efforts of museum experts have been focused on the research of inhabitants of protected territories and on the rare and endangered species.

The museum exhibitions occupy 15 halls on 4 floors. It exhibits the Caroline parrot, which became extinct world-wide, the monk seal, bearded vulture, little bustard, grey and maiden crane, steppe viper, German sturgeon, all of which extinct in Bulgaria. In recent years several dioramas were added to the exhibitions depicting the live nature of the Arctic (white bears and seals), Africa (black panther), Asia (tiger) and South American tropical forest (jaguar, ara parrots, tamarine monkeys). Other large mammals recently exhibited are the white rhinoceros, the Himalayan bear, cheetahs, buffalos.

The visitors are intrigued by one of the last pure-bred aurochs found in nature, the brown bear proclaimed as the largest in Europe, the rare small panda, the beautiful birds of paradise, toucans, the Californian condor extinct in the wild nature, the different types of pheasants with splendid feathers, the giant African tortoise, the blind cave fish from America, the Periophtalmus fish, which can move on land as well.

In the Asenovgrad branch the visitors can see casts of a Deinotherium skeleton, one of the largest terrestrial mammals of all times, 6.80 m long and 4.50 m tall. There are also skeletons of sabertooth tiger, hipparions, antelopes, mastodons, monkeys.