Room I
Neolithic period (5000-2600 BC): Pottery, figurines and tools from Neolithic sites in central and east Crete. Pre-palatial period (2600-1900 BC): Pottery of various styles, stone vases, seals, figurines and jewellery from Pre-palatial settlements and tombs.

Room II
Old Palace period (1900-1700 BC): Finds from the palaces at Knossos and Malia, and votive and cult objects from peak sanctuaries.

Room III
Old Palace period (1900-1700 BC): Finds from the palace at Phaistos, Kamares ware vases, clay sealings, the Phaistos disk, cult objects.

Room IV
New Palace period (1700-1450 BC): Finds from the palaces at Knossos, Phaistos and Malia.

Room V
Late Palace period (1450-1400 BC): Finds from the region of Knossos, clay Linear A and B tablets, 'palace' style and 'floral' style pottery.

Room VI
Finds from the New Palace and Post-palace cemeteries at Knossos and Phaistos (1450-1300 BC).

Room VII
New Palace period (1700-1450 BC): Finds from megara, villas and caves in central Crete.

Room VIII
Finds from the palace at Zakros (1700-1450 BC).

Room IX
Finds from New Palace settlements in east Crete (1700-1450 BC) (Palaikastro, Gournia, Pseira, etc).

Room X
Post-palace period (1400-1150 BC): Finds from Knossos, Phaistos, Gortys, Siteia, etc.

Room XI
Sub-Minoan and early Geometric periods (1150-800 BC): Finds from various sites in Crete and the cemeteries at Prinias, the tombs at Fortetsa - Knossos, the Cave of the goddess Eileithyia at Inatos, etc.

Room XII
Geometric and Oriental periods (800-650 BC): Finds from the sanctuary at Symi Viannou and from tombs at Knossos, Arkades, Fortetsa, etc.

Room XIII(Vestibule)
Collection of painted clay sarcophagi belonging to Post-palace times (1400-1150 BC).

First Floor

Room XIV-XVI
Display of Minoan wall paintings (1600-1400BC) from the palace at Knossos, the villas at Agia Triada, Amnissos, etc.

Room XVII
Exhibits from the Yamalakis Collection dating from the Neolithic to the Venetian period.

Room XVIII
Greek and Roman sculpture, pottery and miniature art (7th c. BC-4th c.AD) from Gortys, Praisos, etc.

Room XIX
Collection of sculpture of the archaic period (7th-6th c. BC). Words of early 'Daidalic' sculpture and Archaic metalwork.

Room XX
Classical, Hellenistic and Roman sculpture from Gortys, Knossos, Chersonisos, etc. (5th c. BC-4th C. AD).