Already during the first decades of the Museum’s istory, the institute was split into several smaller, more or less independent sections. The five sections were each responsible for one of the collection: the botanical, the mineralogical, the paleontological, the anthropological, and the zoological collections.

The independent Museum of Paleontology and Geology was founded in 1906. In that time, it was housed on the ground floor of a small building at the corner of Academia and Sina Street in the centre of Athens. Its main exhibition was housed in an elongated hall which was barely sufficient for the exposition of a general geological and paleontological collection. The majority of the material was stored at two rooms in the basement of a nearby building of the Law School.

That building does not exist anymore, and in its place came the garden of the building next door. In 1981 the Museum was moved to its present location in the buildings of the university campus outside Athens. The Museum is housed in the same building as the
Faculty of Geology and Geoenvironment.