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The Museum is located on the Castle of Lipari and is divided into several restored historic buildings, in addition to the twentieth-century buildings of the fascist confinement camp. The exhibition itinerary is developed in six thematic pavilions which illustrate the development of human settlements and the history of successive civilizations in the Aeolian Archipelago, through the numerous finds dating from Prehistory to the Modern Age:


1) History of the Museum and excavations
2) Prehistory of Lipari and foundation of the Greek city
3) Prehistory of the smaller islands
4) Epigraphy
5) Greek and Roman age
6) Volcanology that illustrates the geomorphological features of the Aeolian Islands.


In 2014, the former prison was chosen to host a permanent exhibition of contemporary art "Mare Motus" and added to these pavilions. The artists, including Mitoraj, Ben Jelloun and Plessi, have collected their installations on the theme of freedom, the sea and escape.
The archaeological collections have the particularity of all deriving from archaeological excavations carried out from 1950 to today in the archipelago. For this reason, each artefact exhibited transmits its evocative power by telling the story of the past. Each exhibit is linked to a context of origin; site, layer, hut, house, tomb, sanctuary, wreck. The material and cultural wealth of the Aeolian Islands is evident in the rooms of the Museum to be explored in chronological order starting from the most ancient Neolithic (5500-5000 BC), through the Bronze Age, towards the Greek and Roman age when the city is organized topographically with Acropolis, city of the living and city of the dead. Almost 3,000 tombs come from the latter, the necropolis, whose grave goods tell of myths, religions, tastes, traditions, aspects of life at that time. The red-figure craters stand out with representations related to the world of Dionysus and the hall of theatrical masks of ancient and new tragedy and comedy and satyric drama. One sector is dedicated to underwater archeology with reconstructions of the loads of Greek and Roman ships sunk in the Aeolian waters.

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