It is the kind of detail that hints at how much of the town's medieval fabric persists beneath its later skin. Buildings along O'Connell Street, Collet's Lane, and at the West Gate carry late sixteenth and early seventeenth-century features that have been obscured by subsequent phases of construction, and it is thought that many other Clonmel buildings have considerably earlier origins than their Georgian or Victorian facades would suggest. Even the road widens slightly at the western end of the main street, not by accident but to accommodate what was once called 'Middle Row', a block of houses built down the centre of the street between Mary Street and the West Gate.

The town's origins lie in a grant to William de Burgo in 1205 or 1206, though it was probably his son Richard who actually established the settlement on the north bank of the River Suir. Henry III granted Richard the right to hold an annual fair in 1225, and by 1265 the manor had passed to Otho de Grandison, who also founded the Franciscan friary in the south-east corner of the town in 1269. A murage grant of 1298, one of the earliest recorded, provided funding for the town walls, a system of taxation levied on goods passing through a town specifically to pay for its defences. Further grants followed through the fourteenth and into the fifteenth century. Clonmel became the caput, or administrative capital, of the County Palatine in 1328, a quasi-independent jurisdiction controlled by the Earls of Ormond, a status it held until the Palatinate was extinguished by Act of Parliament in 1712. The town changed hands repeatedly across the intervening centuries, passing from the Fitzgeralds to the Butlers around 1531 as part of a marriage settlement, surviving siege after siege, hosting the Supreme Council of the Confederation of Kilkenny in 1647, and enduring Cromwell's assault in 1650. After the Restoration, the Duke of Ormond imported some 500 families from Canterbury in 1665 to establish a woollen industry, and a new Palatinate courthouse, the Main Guard, was built in 1662 to replace the court building destroyed during the siege.

Below street level, excavations have added another layer to the picture. Medieval middens, rubbish deposits and deliberate ground-raising episodes have been identified behind properties along the main streets, including evidence that land beside the Suir at the rear of 35 to 36 O'Connell Street was raised in the fourteenth century, apparently to bring it up to the level of the newly built town wall. Digs on Upper Gladstone Street, outside the walled circuit, turned up cultivated garden soil rather than suburban housing, confirming that the area immediately beyond the walls was open agricultural land in the medieval period. A stretch of probable cultivation furrows was also found near the north-east mural tower on Kickham Street, roughly twenty metres beyond the wall line, a quiet reminder that even a besieged and battered medieval town needed to grow things.