As far back as ancient times, pilgrims left graffiti with entreaties, prayers or simply names, along the walls of the place of worship, an age-old tradition that has carried on through to modern times.

The museum holds exhibits of the oldest graffiti, dating back to the pre-Byzantine period.

In a casket at the centre of the room, the most representative finding is on display, found in the digs below the Byzantine mosaics. It is the base of a column, bearing the graffiti, in Greek, so-called “KAIRE MARIA”, the oldest Marian invocation known until now. It is written in the abbreviated form, "XE MAPYA", and means “Hail Mary”. This base was part of the pre-Byzantine structure and is testimony to the long and important Marian worship at the Holy Grotto. Other graffiti can be found on the same stone, including two words written in Armenian, the meaning of which is subject to debate.

Two separate showcases conserve other important graffiti, one with a Greek inscription reciting “in the holy place of M(ary), I wrote ”, and one with a representation of a man standing holding a standard. This carving is open to various interpretations: some believe that it is John the Baptist and others believe it is an angel. Now, on seeing the outlines of the image, it is thought that the figure is that of a pilgrim, perhaps a soldier, who left this graffiti as testimony to his passing through this holy place.

Along the left wall visitors can admire at least thirteen stones belonging to the pre-Byzantine building. The plaster bears various inscriptions and names of pilgrims, from which we can recognise those of Zeninoi, Ruth, Leones, Naukida, and Ananias.