The Museum of the Ancient Agora is housed in the Stoa of Attalos, which was reconstructed according to the designs of the architect of the excavations made by the American School of Classical Studies, Ioannis Travlos, in 1957. Henceforth, all the findings from the excavations conducted by the American School since 1931have been gathered in the area. The exhibition also includes the ground floor.

The museum collection is characterized by a plethora of objects which pertain with the function of the democratic regime of Athens: one can see many ostraca (potsherds), on which are carved the names of known politicians of Ancient Athens who have been threatened or punished with exile, through this special procedure known as ostracism. One can find the names of Pericles, his father Xanthippos, Aristides, Kallias, Megaklis of the family of Alkmaeonidae, Ipparchos, grandson of the tyrant Ippias, and many more historical figures. Other significant findings include a water clock (klepsydra) from the 5th century, that is a clock which was used to count the time of speeches in the public courts, copper votes used by judges for their verdict during the 4th century, as well as the cleroterion (allotment machine) from the 3rd-2nd century B.C., when the citizens were divided into twelve tribes. The city’s glorious military history is demonstrated by the copper shield which bears an inscription stating that it was taken as loot by the Athenians from the Spartan hostages in Sfaktiria in 425-424 B.C. 

The inscriptions hold a significant position among the findings, dating from the 5th until the 2nd century and referring to many aspects of the public life in Athens. Worth mentioning are the list of horses from the records of the riders and a signed stele bearing the voting of Phrynichos against tyranny.

The commercial aspect of the Agora is demonstrated by the various coins in exhibition: all Athens coinage is included as well as a plethora of coins from other states, showing the breadth of the city’s commercial activities at its prime (5th – 4th century B.C.) Another element demonstrating the Agora’s commercial character is the small number of amphorae under exhibit, which gives an idea of the thousand amphorae, often with stamped handles, which were found in Athens. The amphorae are dating back to the 6th century until the Byzantine era.  

The majority of the findings come, of course, from the graves that were in the Agora from prehistoric times until the end of the 6th century. Particularly important are the group of graves of the wealthy Athenian woman or the grave of the Warrior. The great collection of black-figure and red-figure vessels of the archaic and classical period is equally interesting, and it comes from the wells excavated by the Americans. The sample is particularly characteristic and offers a panorama of the period's angiography. Aside from the vessels that were found in the Agora, also worth noting is the calyx-crater attributed to Exekias which comes from the Western Incline of the Acropolis. Also worth noting are the ceramic findings from the early 5th century from the recently excavated apothetes in the area of the altar of Venus.

Sculptures from the classical, Hellenistic and roman period, as well as architectural members, are exhibited in the ground floor and the first floor peristyle of the Stoa. Among these sculptures, it is worth mentioning the Running Nereid, possibly an acroterion from 400 B.C., in the style of sculptor Timotheos, hermaic steles, Roman portraits and Ionian capitals from temples of the 5th century which were transferred to Agora from other parts of Attica. Worth mentioning from the roman period is the collection of sculptures from the Οικία Ωμέφα, the Iliad and the Odyssey from the Library of Pantainos as well as the hermaic stele with the figure of the sleepy Selenos.

The workshops of maintenance and study of the findings as well as the various models of the area and the Agora monuments that have been made through the years are housed on the first floor.