The museum was founded in 1810 together with the Humboldt University and has been located in the building on Invalidenstraße since 1889. With over 25 million objects, it houses the largest German collections in the fields of zoology, palaeontology and mineralogy.

Its most famous exhibits are the skeleton of Brachiosaurus brancai, the largest dinosaur skeleton in the world at over 13 metres high, and the Berlin specimen of the prehistoric bird Archaeopteryx. The newly designed dinosaur hall and permanent exhibitions on the cosmos and the solar system, the formation of the earth and the mechanisms of evolution opened in 2007.

The "Biodiversity Wall" with around 3,000 prepared animal species illustrates how new species are created. In an originally preserved room from the 19th century, 1,077 mineral species are exhibited, including pieces from Alexander von Humboldt's collection. Native animals can also be seen in large dioramas.

Since 2010, a research collection has been accessible in the east wing of the building: the zoological alcohol collections with around one million objects - fish, spiders, crustaceans