The rare exhibits are displayed in six large halls.
GALLERY 1: Visitors become acquainted with the Neolithic period as this is represented by the nearby Cave 
of Pan. After the battle of Marathon, Pan was worshipped as a hero in the region because he had assisted the Athenians. 
GALLERY 2: The second gallery includes objects dating to the 3rd millennium (Early Bronze Age). Exhibits come 
from the famous Early Helladic cemetery at Tsepi, the Prehistoric tumuli at Vranas, and the Mycenaean chamber tomb at Arnos. 
GALLERY 3: In this gallery are exhibited finds coming chiefly from tombs representing the Geometric, Archaic, and Classical periods. The black- and red-figured vases, grave offerings from the corresponding cemeteries in the area, are of superb quality, in no way inferior to their contemporary Athenian counterparts. 
GALLERY 4: This gallery includes portraits of the famous Marathonian sophist Herodes Atticus (2nd c. AD), his students, as well as architectural members and seated portrait statues of Herodes and Regilla (his wife) from their estate, at the site “Mandra tis Grias”, a little north of Vranas. 
GALLERY 5: A particularly evocative gallery, since its Egyptianizing exhibits from the sanctuary of the Egyptian gods at Brexiza in nearby Nea Marki are truly unique. The founding of the sanctuary and the adjacent bath-house were owed to Herodes Atticus. 
GALLERY 6: The last gallery is called the “trophy gallery”, since it is dominated by part of the trophy set up  in the plain of Marathon following the Athenians’ victory over the Persians in 590 BC. Two display cases include grave offerings from the tumulus of the Athenians and the so-called “Tumulus of the Plataeans”. The funerary reliefs and inscriptions on display date to the Classical period.
Source: www.tap.gr/tapadb/components/com_jshopping/files/demo_products/025_MMA_Mouseio_Marathona_W.pdf