The collection for arachnids is one of the largest and oldest of its kind in Europe. With regards to some groups (scorpions, spiders and mites) it is one of the most important collections internationally and is constantly being expanded through current research projects. For example, the cabinets contain one of the world's largest collections of scorpions. It also holds the famous Godeffroy collection of spiders from Australia and the Pacific region, which was collected almost 160 years ago on behalf of the famous Hamburg merchant Johann Cesar Godeffroy and comprises several thousand species. There is also a complete collection of all spider species occurring in Germany, as well as an important reference collection of mites with more than 32,500 specimens. Currently, a collection of spiders in the Hamburg area is being established, as well as the expansion of existing collections from South America and Australia.

The collection is the largest German collection of crustaceans and houses approximately 850,000 individuals of over 7,100 crustacean species. The scientific material includes significant historical material, including from the Gazelle and Challenger expeditions and from the Godeffroy and Pfeffer collections. More than 90% of the species in the collection come from the sea (especially the Southern Hemisphere); while the rest includes freshwater, terrestrial, and even fossil material. The biogeographic focus is on the southern continent, Polar Regions, and the deep sea. Research focuses on the systematics, biogeography, and evolution of Ostracoda, Copepoda, Peracarida (Isopoda, Amphipoda, Cumacea, Tanaidaea), and Decapoda.

The collection contains more than 65,000 species with about 5 million individuals. After almost complete destruction of the collection of holometabols (e.g. beetles, wasps, butterflies) and only partial preservation of the hemimetabol collection (e.g. crickets, bugs, dragonflies) during the Second World War, the entomological collection has grown back to one of the most important entomological collections in Germany through acquisitions, collaborations and own collections. With approx. 10,000 type specimens and a strong North German focus, the collection is of high scientific value. Its ancient heritage also makes it of inestimable cultural value, as it represents the legacy of members of the Hamburg Natural Science Association of the early 19th century.

The geological-paleontological collections date back to the collections of the Geological State Institute, founded in 1907, which in turn emerged from the mineralogical and geological-paleontological collections of the former Natural History Museum in Hamburg. The collection contributes to a fundamental understanding of the connections between geological processes, climate change, evolution and the development of species diversity in Europe.

The Herpetological Collection is the fifth largest German collection of amphibians and reptiles and contains about 90.000 specimens. The collection consists of 70 % reptiles and 30 % amphibians, stored essentially in jars filled with ethanol, supplemented by several hundred dried skeleton and skin specimens and more than 300 sets of serial histological sections. The collection is characterized by a high proportion of specimens from the 19th century. The oldest specimens are South American snakes collected and described by Prince Maximilian zu Wied-Neuwied (1782-1867). Several extinct species such as the Mauritius boa and Cape Verdean giant skink are held in the collection. The valuable Australian collections of Amalie Dietrich (1821-1891) set an additional highlight.

The collection contains over 8,000 fish species in over 1,300 type series (42% of which are primary types) from all oceans and all continents. Thus about a quarter of all known fish species and two thirds of all Atlantic fish species are represented. It is the largest fish collection in Germany with extinct fish species from Europe and North America and precious specimens from the 19th century, e.g. from collections of Godeffroy and Bleeker. The oldest collection object dates from 1838.

The collection contains material from all continents and all oceans. Important focal points of the collection are land snails from South-Eastern Europe and the Near East, North-Western South America (Colombia, Peru) and East Africa (Uganda), freshwater molluscs from Thailand and marine molluscs from the Antarctic and Patagonian regions. The collection is regularly growing due to the catches of research vessels ("Walter Herwig", "Polarstern") and the acquisition of private collections.

The collection is one of the most important collections of its kind in Germany, with 10,000 counts of skeletal material and 5,000 counts of material preserved in alcohol, mainly large mammals. The collection focuses on bovidae and whales, odd-toed ungulates, primates, predators, marine mammals and bats. In total, the mammal collection houses more than 17,000 individuals. The collection of brains is of great importance.

Minerals, precious stones, meteorites, ores and rocks: The Mineralogical Collection of the University of Hamburg comprises around 90,000 objects, making it one of the largest of its kind in Germany. The comprehensive reference collections form the basis of the University's geoscientific education and research.

The extensive ornithological collection comprises 3,500 species. This includes extensive historical material and parts of the Godeffroy Museum's ornithological collection from the South Pacific. Geographical focal points are: Germany, Sao Tomé, Far East of Russia, China, Angola, East Africa, India, Pacific, Peru, Ecuador, Guatemala, Philippines, New Guinea, Australia, the Bismarck Archipelago and feathers of birds of the West Palearctic. Noteworthy is the large collection of magpies (Pica pica) from all over Europe.

The collection includes all multicellular animals not belonging to vertebrates, arthropods, molluscs or annelids. These include sponges, cnidarians, several worm-like groups (flatworms, roundworms and others), echinoderms and tunicates. Parts of the collections are of international importance, for example marine nematods, horsehair worms (nematomorphs), arrow worms (chaetognaths), freshwater moss animals (bryozoans) as well as tunicate groups such as sea squirts (Ascidia).