The building's most recent use is widely agreed to have been an assembly hall for Jews or Samaritans. However, the first use for the building is more controversial. While some people think the building was erected as a private house or a pagan meeting place, most believe that it was a synagogue even in its earliest form.
Located on the eastern side of the city of Delos, the synagogue was far from the central areas of the city. Instead, the synagogue was built in a section of Delos called the Quartier du stade. In this part of the city, in contrast to the religious and commercial focus at Delos' center, residences dominated the scene (there was also a small, easily accessible port).
The synagogue itself consisted of two large rooms containing a throne and multiple marble benches as well as many smaller rooms which allowed for access to a reservoir.
The synagogue was discovered in 1912 by a team led by archaeologist André Plassart. The synagogue is understood to have remained in use until the end of the second century AD. The dominating feature of the building is the large hall, which was presumably used in a flexible way, with moveable furniture, since there is no evidence for benches built along the walls. The hall is oriented towards the east, with a series of secondary rooms at the southern end.
The identification of the building as a Jewish synagogue at any point in its history has been a matter of debate. The original identification of the building as a synagogue by Plassart was based in large part on dedicatory inscriptions referring to "Theos Hypsistos," or "God Most High," often considered an appellation for the Jewish God in antiquity, though not exclusively. The identification of the building as a synagogue was originally challenged by Belle Mazur in 1935, though this argument has gone largely unnoticed by more recent scholarship. The evidence of "synagogue's" architecture and inscriptions is complicated by the apparent presence of a contemporary Samaritan community not far. More recent studies have concluded that the evidence suggesting that this building was indeed a synagogue is tenuous at best and will no doubt remain an open question.