The Basilica of St. Mary was built in the middle or end of the 4th century in Ephesus. While it is now in ruins, its plan is still very visible, revealing a massive basilical church. It served as the cathedral of Ephesus and was the location of the councils held in Ephesus in 431 and 449.

The site had previously been the location of a market basilica that the Goths had a century earlier. The ruins were rebuilt and converted into a great church - a three-aisled, apsed basilica with narthex and a large atrium. It was constructed of well-cut stones, including many spoils and brick, and incorporated the foundations and part of the walls of the solidly built earlier market. The interior seems to have been decorated with some magnificence; the floors were paved with marble and mosaic of geometric design, the walls were rescued with marble. The atrium, an open colonnaded court which occupied the west end of the former market, clearly showed the tendency of the times to use whatever material was at hand even for the most splendid constructions. Columns of varying heights were reused, bases and capitals rarely matched; the marble paving included numerous old inscriptions, some of which may still be read. This atrium gave access to a large, domed, octagonal baptistery neatly constructed of brick and cut stone. The interior centered on a recessed basin for baptism by immersion which was reached by a small flight of steps; the space around was decorated by blocks of marble with huge crosses in relief.

At a later date, the church was rebuilt into a domed basilica, which also seems to have falling into ruins and later replaced by a smaller church. The new basilica, which used piers to support in ruin was built into the space between the apse of the domed church and that of the original cathedral. The apse of the old church was cut through to provide an entrance portal, its nave served as an atrium and its diaconicon as a baptistery for the new church, which itself showed signs of decline and poverty. It employed walled-up arcades instead of colonnades, and included reused material of all kinds, as well as a good deal of wood. A small room added to the south side may have functioned as a burial chapel; it was decorated with a fresco showing a jeweled cross and geometric designs.
Other parts of the complex were converted to profane uses. Ovens were built into the former Baptist, and west apse. A small bath erected in the north colonnade of the atrium is perhaps also to be associated with this period. It consisted of a few narrow rooms, one of which contained a hypocaust. These buildings may suggest that part of the great arc of the late antique church had been turned into a residential district. At the same time, a cemetery grew up around the church, which seems by this time to have declined to be the graveyard church of the city.
Subsequently, the small basilica was rebuilt by the addition of two rows of columns to support the roof, making the church into a five-aisled basilica. Ultimately, after its final collapse, the whole building was used as a graveyard. The chronology of these developments is quite uncertain. Both stages of the basilica on piers are generally presumed to be later than the domed church, and may have antedated the shift of the center of Ephesus to Ayasuluk. In any case, it is evident that there was still a substantial settlement and some activity in this part of the city in the Middle Byzantine period.