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The department comprises the Geology Section, the Zoology Section, and the Botany Section. The rich collections of the department contain living organisms and non-living matter found in Bosnia and Herzegovina and other countries.

The organisation and systematisation of collections at the Archaeology Department is based on classical chronological divisions, thus the department itself is divided into three sections: the Prehistory Section, the Classical Antiquity Section and the Middle Ages Section.

The Ethnology Department collects, maintains, exhibits, and studies all items of material, spiritual, and social culture of the peoples of Bosnia and Herzegovina. It has a rich collection of material which is stored or arranged into thematic exhibitions.