In August 1994 an image was said to have become visible on a wall behind the altar of the 137 year old stone church. It was interpreted as an uncannily clear image of the Virgin Mary, depicting her face and features, her shoulders and abdomen. She appeared to be holding the crucified Christ in the manner of a pieta. Her gaze is directed toward the tabernacle immediately below containing the eucharistic bread. At her lower side is a rose, a symbol of the Virgin Mary.
Two years after the image appeared on the wall the local press covered the story in the Adelaide Advertiser. Within a few days the world media descended on the small oceanside town and the first pilgrims began arriving from Australia and overseas.
In December 1996 the Bishop of The Murray blessed the church as "The Shrine of Our Lady of Yankalilla". The Canadian-born parish priest, Andrew Notere, was involved for the next ten years in developing the church as a pilgrimage centre. A number of documentaries were made. One, Visions of Yankalilla, has been screened on a wide variety of national broadcasting systems around the world.
The shrine has become the centre of a healing ministry and has been the venue of a number of sightings of the Virgin, as well as several photos of the Madonna in the church.
A well for holy water is on the site, and a hybrid rose has been cultivated called "Our Lady of Yankalilla". The South Australia Tourism Commission has developed a marketing brochure for the shrine entitled, Mary Among the Eucalypts. The Australian artist Pro Hart donated a painting to the shrine and a large mural of the Virgin of Yankalilla has been mounted on an exterior wall of the retreat centre adjacent to the church.