Excavations carried out in 1994 and 1995 to the rear of the Main Guard courthouse brought them to light: burials in unmarked pits, without coffins, laid out on an east-west axis with the heads almost universally to the west, a orientation consistent with Christian burial practice. Several skeletons were only partially intact, and a considerable quantity of disarticulated bones was recovered alongside them, the disruption a consequence of the very building work that had covered them over in the first place.

The story of how those remains came to be disturbed is, in its own way, a compressed history of Clonmel itself. The burial ground almost certainly began as the graveyard of a Franciscan friary founded on the site in 1269. When Henry VIII's Dissolution of the Monasteries reached the friary in 1540, the church and its graveyard passed into the hands of the citizens of Clonmel rather than being abandoned outright, and burials appear to have continued there for well over a century after the friars departed. That arrangement came to an end in the early 1670s, when the ground was acquired for the construction of the Main Guard, a building erected under the Duke of Ormond's patronage as a combined courthouse and military guardhouse. Further disturbance followed in the 1800s, when the return block of the Main Guard was subdivided and new buildings were added. None of the skeletons yielded datable objects, so the precise span of the burial ground's use cannot be fixed with certainty, but the sequence fits: a medieval friary cemetery, repurposed after the Reformation, then quietly built over as the town reshaped itself around the demands of a new century.