- The emergence of the sanctuary and the early offerings (Rooms I-II)
This unit presents the early years of the sanctuary, before the establishment of the cult of Apollo, and the transition to a new area and new cult. Mycenaean figurines and Minoan stone rhyta are displayed with bronze tripods, the earliest offerings to the new deity. Creto-Cypriot shields, a Phoenician bowl, Phrygian fibulae and Syrian sirens are among the early bronze offerings. A series of votive male figurines of the Geometric period completes the display in Room I. Room II contains the remaining bronze offerings of the eighth and seventh centuries BC: animal figurines, women's jewellery, votive helmets and the famous 'daedalic kouros', a small bronze precursor of the large-scale marble statues of the sixth century, presented in Room III.
- The early Archaic period (Room III)
The twin kouroi, a selection of bronze objects of the same period and the tufa frieze of the Sikyonian Treasury are displayed in this unit.
- The Sacred Way votive pit (Room IV)
The finds from the votive pit of the Sacred Way are representative of the offerings dedicated by the Eastern Greek cities in the Archaic period. The display also includes the Apollonian Triad and a silver bull.
- The Siphnian Treasury (Room V)
This unit presents parts of the architectural sculpture (frieze, east pediment, door jambs and lintel, karyatides) of the Treasury of the Siphnians, the Naxian Sphinx and architectural sculpture from other buildings of the sanctuary.
- The Temple of Apollo (Room VI)
Architectural elements of the Temple of Apollo, including the pedimental statuary of the Archaic and Classical temples, comprise this unit.
- The Athenian Treasury (Rooms VII-VIII)
The sculptural decoration of the Treasury of the Athenians comprises this unit. Room VII contains the frieze and metopes, while the two preserved acroteria representing Amazons on horseback, parts of the pediments and the later inscriptions with the hymns to Apollo are presented in Room VIII.
- Offerings of the fifth century BC (Room IX)
This unit presents a selection of offerings of the fifth century BC, including the sculptural and terracotta painted decoration of the two treasuries of the sanctuary of Athena Pronaia (Treasury of Massalia and the Doric Treasury), acroteria from the other buildings of this sanctuary and characteristic waterspouts and antefixes from both sanctuaries. It also presents the three bronze statues found in the votive pit of the Sacred Way: a 'peplophoros' holding an incense burner, a man playing the flute and a group of two athletes. A female head from the sanctuary of Athena Pronaia completes the display and heralds the transition to the fourth century BC.
- The Tholos (Room X)
This room is dedicated to the Tholos, the circular building in the sanctuary of Athena Pronaia. The display consists of architectural elements and parts of the building's sculptural decoration, including two characteristic capitals, one Doric and one Corinthian, the metopes and the two friezes.
- Late Classical and Hellenistic periods (Room XI)
The offering of Daochos, the Omphalos and the column with the dancing girls dominate the display. A series of Late Classical and Hellenistic statues illustrate the wealth of the offerings donated to the sanctuary.
- Late Hellenistic and Roman periods (Room XII)
The frieze of the offering of Aemilius Paulus, the first in a series of Roman monuments of the sanctuary, dominates Room XII. Several Late Hellenistic and Roman works, such as the circular altar of the Pronaia, the statue of Antinoos, the alleged portrait of Titus Flamininus and representative examples of Roman metalwork complete the display.
- The Charioteer (Room XIII)
This room is dedicated to the Charioteer one of the most famous and most important exhibits of the museum.
- The end of the sanctuary (Room XIV)
This unit illustrates the last centuries of the sanctuary through inscriptions and portraits of Roman emperors, and architectural elements and lamps with Christian symbols, characteristic of the transition to the new religion.