The aim of the Estonian Museum of Natural History is to collect and preserve the diversity of nature in Estonia and document the temporal and spatial changes therein. The collections of the Estonian Museum of Natural History contain about 320,000 museum specimens.

Approximately 90% of the plant, beetle, butterfly and moth, bird and mammal species found in Estonia are represented in the collections. 

A highly valuable part of the collections is made up by type specimens – the specimens used to provide the first description of a new taxon and serving as a definitive example of that taxon.

The museum also has a photo and video collection that consists of 300,000 specimens and a history of science collection.

The collections of the museum are used in research and educational work and for composing exhibitions. The collections can be used in-house. Lending of specimens for scientific examination is also possible.