The exhibition is structured in four units, referring to the history of research at Thera, the geology of Thera, the island's history from the Late Neolithic to the Late Cycladic I periond (early 17th century B.C.) and the heyday of the city at Akrotiri (mature Late Cycladic I period, 17th century B.C.). In the last unit, in particular, various aspects are presented, such as the plan and architecture of the city and its organization as an urban centre, the emergent bureaucratic system, the development of the monumental art of wall-painting, the rich and diverse pottery repertoire, the elegant jewellery, the reciprocal influences between vase-painting and wall-painting, and the city's and the island's complex network of contacts with the outside word.

The exhibits include fossils of plants that flourished before the human habitation of Thera and archaeological objects. Among the earliest pieces are Neolithic pottery, Early Cycladic marble figurines, Early Cycladic pottery, including interesting pieces of the transitional phase from Late Cycladic II to Late Cycladic III period (Kastri group) from the Christiana islets and Akrotiri (3300-2000 B.C.) -Middle Cycladic pottery with a series of impressive bird jugs, many of them decorated with swallows - from Ftellos, Megalochori and Akrotiri (20th-18th century B.C.), and Early Cycladic metal artefacts from the last two sites.

The exhibition endeavours to sketch the course of Thera in prehistoric times, through selected finds from the thousands in the storerooms. This was a dynamic and creative course which established the city at Akrotiri as one of the most important Aegean centres during the 18th and 17th centuries B.C.