The original core of the Museum's collections derives from the activity of the Geo-palaeontology Group of Empoli. In the late Eighties, in consideration of the large amount of material collected and the lack of suitable facilities for its conservation and use for educational purposes, the Commune of Empoli decided to establish a Civic Museum, located in Palazzo Ghibellino, entrusting its management to the GeA Association.

The Museum contains fossils and rocks which document the history of the Earth. The most consistent core of the collection is made up of fossils coming from Tuscan localities with sedimentation outcrops from the Mesozoic and Caenozoic ages. Of special interest are the malacoid fauna found in the Pliocene deposits emerging in the basins of the Arno, Cecina and Ombrone rivers. The Museum also possesses various models and a life-size diorama displaying a scene of struggle between two dinosaurs.

For schools and organised groups, the GeA Association holds guided tours, educational encounters in areas of geo-palaeontological and naturalist interest (the old Spicchio e Arno Vecchio Quarry) and courses in environmental education, supplemented by practical activities in the laboratory annexed to the Museum.