The excavations on the complex known locally as Üçgözler (three eyes) were initially carried out between 1883 and 1888 by members of the German Oriental Committee. The second excavations were carried out between 1902 and 1903, and lasted only one to two weeks, aimed at finding missing fragments of caryatid and nymph sculptures uncovered after the 1899 earthquake.

The first excavation with scientific aims was started in 1996 by the Adnan Menderes University and continues to this day, with the focus on the approx. 25,000 square metre bath gymnastics complex from the Roman Empire. Excavation results indicate that there was already an earlier monumental gymnasium building in the area of the now visible Bad-Gymnasium complex, which was destroyed by an earthquake in 26 B.C. In the early 1st century A.D. the building regained its importance after reconstruction under Antoninus Pius (138-161 A.D.).

Jewish lamps found during the excavations may indicate the presence of a Jewish synagogue, probably built at the beginning of the third century AD, in the south of the grammar school building.

During the five years of the excavations of the University of Menderes, part of the caldarium, the latrine and a large hall of the bath building were uncovered.

The complex in Tralleis is reminiscent of the Bad-Gymnasium complex in Sardis. The Tralleis complex underwent reconstructions, modifications and additions, especially in the early Byzantine period. It was probably abandoned after the Sassanian Persian invasion in 616 AD, but was used as a late Byzantine settlement between the ninth and fourteenth centuries.