After the interrogation and the eventual absolution awarded by the priest or official the candidate was brought into the Hiéron, which also functioned as an épopteion, or "place of contemplation", where ritual cleansing took place and sacrifice was made into a sacred hearth located in the center of the "holy of holies".

The initiate then went to an apse in the rear of the building, which was probably intended to resemble a grotto. The hiérophante (hierophántês), otherwise known as the initiator, took his place on a platform (bêma), in the apse where he recited the liturgy and displayed the symbols of the mysteries.

During the Roman era, towards 200 AD, the entrance to the Hiéron was modified to permit the entrance of live sacrificial offerings.

A parapet was constructed in the interior to protect the spectators and a crypt was fitted into the apse.

These modifications permitted the celebration of the Kriobolia and the Taurobolia of the Anatolian Magna Mater, which were introduced to the épopteia at this time. The new rites saw the initiate or possibly only the priest in by proxy, descend into a pit in the apse. The blood of the sacrificial animals then flowed over him or her in the fashion of a baptismal rite.

The Samothrace site may appear to be somewhat confusing at first glance; this is due to a combination of the unusual topography and the two century long period over which the site was developed.

The sanctuary occupies three narrow terraces on the west slopes of mount Hagios Georgios, separated by two steep-banked torrents.

The entrance is in the east through the Ptolemy II propylaeum, also known as the Ptolémaion (site plan number 20), which spans the eastern brook and functions as a bridge. Immediately to the West, on the first terrace, there is a somewhat circular paved depression, containing an altar in the centre, which was undoubtedly a sacrificial area; although the precise function of this place has not further been determined.

A winding path descends towards the main terrace, between two brooks, where the main monuments to the cult can be found.

A large tholos, the Arsinoéion, or Arsinoé Rotunda (site plan number 15), the largest covered round space in the ancient Greek world (20 m in diameter), may have served to welcome the théores, sacred ambassadors delegated by cities and associations to attend the great festivals at the sanctuary.

The decoration of rosettes and garlanded bull's heads leads some to believe that sacrifices may have also taken place here. The rotunda was built on an older building of which only the foundation has remained.

Right at the opening of the path leading to the sanctuary, one finds the largest building, the Building of the Dancer's Frieze (site plan number 14), sometimes called the Temenos, as it corresponds to a monumental enclosure marking a much older sacrificial area.

There is a great deal of variance in reconstructed plans for this portion of the site (compare for example the different editions of Lehman's archeological guide — the plan used in this article reflects the 4th edition). It is in essence a simple court preceded by an ionic propylaeum decorated with the well-known dancer's frieze (photo below). The celebrated architect Scopas may have been the designer.

The épopteion - Samothrace temple complex