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The ancient Baptismal Font, circa 4th century, is found on the southern side of the main temple. It is the oldest and the best maintained Baptismal Font throughout the Orthodox East, which is why it contains the most important extension of the Ekatontapiliani.
It is a triclinium basilica, measuring 16.50x15 meters, with a dome and a Narthex which connects the main temple and every aisle had been transferred into a chapel for posterity. The vaults and the dome are built of colored limestone, like the main temple and the chapel of St. Nicholas. There is a cross-shaped marble font whose main part is in the ground where the altar is and which was known as "The Inner House" or "Photistirion", the Baptismal Place. There are curved crosses in circles in the section which protrudes from the ground.
The neophyte who entered the font, had to go through the Narthex of the Baptismal Font first, which was known as "The Outer or the Courtyard House". Over there the preparations of rites, exorcisms, the acceptance of the new faith and the recitation of its symbols used to take place. He then proceeded towards the "Photistirion". He went down the font through a small staircase which is situated on the western beam of the cross and which symbolizes his origin from sinful world. After the mystery, he then went up the eastern stairs which symbolizes the entrance of the newly baptized into the true life of Christianity. The priest who officiated these rites stood on pedestals which are found in the middle of the font and are called "Holy Islets". After the baptism, there used to follow the annointment, the dressing of the newly baptized in white clothes and his entrance into the main temple and introduction to Holy Communion. A small column takes the place of the Holy Islet in the Baptismal Font of the Ekatontapiliani, which is there for posterity.
All this occurred during the first centuries of Christianity till the epoch of the Emperor Justin, during whose rule the baptism of children began. Up until then people were baptized at an older age, after having passed the level of catechism and their initiators were persuaded that they were worthy to be believers. The Baptismal Font proves once again and verifies the version that this temple was built in the 4th century.
Some old mosaic floors in the Baptismal Font of the Ekatontapiliani have been saved.
The oldest fresco of the island has been found in the Baptismal Font although not in very good condition with the possible image of St. George. It was painted circa 11th or 12th century.