The department hosts a complete collection of the most characteristic rock types and minerals of the island of Crete, as well as individual collections of rocks and minerals of south Aegean and eastern Mediterranean areas. More than 500 rock samples and 1000 minerals exist at the moment in its collections. Furthermore, representative collections of rocks or/and minerals of Lavrion, Cyprus, and Belgium occur.
Most of the fossils found in the Neogene and Mesozoic rocks of Crete occur in the collections of the department. These fossils consist of plants, molluscs, echinoids, corals, fishes and mammals. The most outstanding among them are the dwarf hippos and elephands, as well as, the recently excavated Deinotherium giganteum from Siteia. Individual collections and samples from the Petrified Forest of Lesvos, the Paleozoic flora of eastern Germany and of the Neogene Paleoflora of Makrylia and Vrysses (Crete) are also hosted.