The MZUSP has one of the largest natural-history collections in Latin America, with over 8.5 million preserved specimens of vertebrates (amphibians, mammals, birds, fish and reptiles) and invertebrates (cnidarians, insects, crustaceans, arachnids, myriapods, annelids, mollusks and other marine groups).

Other facilities in the museum include a library specializing in zoology and laboratories dedicated to research in chronobiology, electron microscopy, molecular biology, histology and CT scans.

In 1890 the Museu Paulista's director, Francisco Mayrink, donated to the São Paulo state government a natural history collection compiled during the 1870s.

During the next 40 years, new research was undertaken based on the growing zoological, botanical, ethnographic and historical collections housed in the Museu Paulista.

During the 1960s several experts were hired; the collection expanded considerably due to research expeditions and prospecting off the southern coast of Brazil by the Oceanographic Institute of the University of São Paulo.

[3] In 2000 the museum's herpetological collection was considered the sixth-largest of its kind,[2] and it is recognized as the largest assemblage of South American reptiles and amphibians.

[4] The herpetological collection began as material from sporadic expeditions by the end of the 19th century, which was still housed in the Museu Paulista.

[2] The ornithological collection also contains tissue samples (about 4,000 items), 2,000 nests, 3,000 eggs, with over 2,000 specimens preserved in wet media.

During this first phase, the collection was curated by zoologist Hermann von Ihering and expeditions were conducted which generated knowledge of the Brazilian avifauna's diversity.

Traveling naturalists associated with the museum explored remote areas (including Juruá in 1902 and other regions of Brazil) and collected specimens.

After 1929, under the curatorship of zoologist Olivério Pinto, activity increased; surveys were conducted in all biomes, in a number of locations.

Under Pinto's many scientific works were published, including Brazilian bird catalogs and the unfinished Ornithologia brasiliense.

In 1930 zoologist Carlos Octaviano da Cunha Vieira became the mammal collection's first curator, remaining in the position until his death in 1958.

After Carvalho's departure the collection did not have an exclusive curator until 1999, when zoologist Mario de Vivo assumed the position.

In 1961 the Department of Zoology hired Gustavo Augusto Schmidt de Melo, who has participated in a number of expeditions emphasizing the collection of decapod crustaceans in marine and continental waters.

[2] The collection is an aggregation of smaller collections focused on individual insect orders, such as Coleoptera (beetles), Diptera (true flies), Hemiptera (true bugs), Hymenoptera (sawflies, wasps, bees and ants), Isoptera (termites) and Lepidoptera (moths and butterflies).

The collection consists primarily of species collected in Brazilian states such as Pará, Mato Grosso Federal District, Mato Grosso do Sul, Goiás, Minas Gerais, Rio de Janeiro, São Paulo, Paraná and Rio Grande do Sul.

The Formicidae (ant) collection is considered the most representative of the neotropical region for its number of type specimens, species diversity and geographical coverage.

Several researchers curated the collection during the 20th century, including Frederico Lange de Morretes (the 1930s), Eveline and Ernst Marcus (the 1950s) and José Luiz Moreira Leme (from the 1960s to the early 2000s).

It includes Annelida, Brachiopoda, Bryozoa, Cestoda, Cephalochordata, Hemichordata, Cnidaria, Ctenophora, Echinodermata, Echiura, Entoprocta, Nematoda, Foraminifera, Phoronida, Rotifera, Turbellaria, Trematoda, Urochordata, Porifera, Priapulida and Sipuncula.

[20] Containing nearly 200,000 lots and 200 type specimens, the collection was built with the efforts of late-19th-century researchers including Ernst and Eveline Marcus, Gilberto Righi, Luis Roberto Tommasi, Antonio Sérgio Ferreira Ditadi, Jeanete Maron Ramos, Gertrude Rita Kloss and Sérgio de Almeida Rodrigues.

[2] The paleontological collection harbors fossils extracted from Brazilian sedimentary basins, including Bauru, São Francisco and Araripe.

[2] In addition to its natural-history collections, the Museum of Zoology has a library and laboratories dedicated to chronobiology, electron microscopy, molecular biology, histology and CT-scans.

[22][23] Its library has one of the most complete zoological collections in South America: over 248,000 volumes (including books, theses and dissertations), scientific journals, specialized magazines, maps, and electronic information-storage media.

When rhythms are detected the neuroanatomy and neurophysiology of specimens are studied, searching for rhythm-generating centers using histology, histochemistry and molecular biology.

Groups studied include springtails (Isotomidae), mosquitoes (Culicidae), crickets (Phalangopsinae), ants (Formicidae) and bees (Apidae).

It covers about 40 acres (96 ha) in a 6,800-acre (16,450-ha) primary forest reserve protecting a watershed about 110 kilometres (68 mi) from the city of São Paulo, in the municipality of Salesópolis.