The rich nature and culture of the Dutch East Indies attracted European intellectuals, scientists and researchers. Some notable scientists that conducted most of their important research in the East Indies archipelago are Teijsmann, Junghuhn, Eijkman,Dubois and Wallace.

Many important art, culture and science institutions were established in Dutch East Indies. For example, the Bataviaasch Genootschap van Kunsten en Wetenschappen, (Royal Batavian Society of Arts and Sciences), the predecessor of the National Museum of Indonesia, was established in 1778 with the aim to promote research and publish findings in the field of arts and sciences, especially history, archaeology, ethnography and physics. The Bogor Botanical Gardens with Herbarium Bogoriense and Museum Zoologicum Bogoriense was a major centre for botanical research established in 1817, with the aim to study the flora and fauna of the archipelago.

Java Man was discovered by Eugène Dubois in 1891. Komodo dragon was first described by Peter Ouwens in 1912, after an aeroplane crash accident in 1911 and rumours about living dinosaurs in Komodo Island in 1910. Vitamin B1 and its relation toberiberi disease was discovered by Eijkman during his work in the Indies.