Geophysical surveying, which uses instruments to detect buried features without breaking the soil, has revealed the traces of a large rectangular stone structure oriented roughly northeast to southwest, measuring approximately 30 metres east to west and 10 metres north to south. It sits about 10 metres east of the cathedral's round tower, that familiar slender landmark of early Irish ecclesiastical sites, and it has never been excavated.

What makes this particularly intriguing is the suggestion, developed by Cóilín Ó Drisceoil in 2004, that this buried structure may have been the direct predecessor of the present 13th-century cathedral rather than a secondary or ancillary building. During restoration works at the cathedral in the 19th century, a separate set of foundations was uncovered and recorded by Graves and Prim in 1857. The geophysics points to something different again, a building of considerable scale that does not correspond to those earlier discoveries. If the interpretation is correct, this rectangular outline in the earth could represent the early medieval church around which the whole subsequent history of the site was organised, replaced over centuries by the Gothic structure that stands today.