From the fourteenth to the seventeenth centuries the Church, like the Anglo-Irish, became more and more removed from English influence and control. The religious orders – Cistercians, Dominicans, Franciscans and Augustinians – which had arrived with the English invasion had been instrumental in reforming the Irish Church, helping to enforce the payment of tithes and establishing a diocesan episcopate and a parochial system. However, by the early thirteenth century, the discipline and practices of the Irish Church had degenerated, and the Synod of Kells’ acceptance of papal authority subordinated the Irish Church to the papacy at the most sordid period in the history of the popes. As early as 1221, a visiting French monk noted, ‘In the abbeys of this country the severity of Cistercian discipline and order is observed in scarcely anything but the wearing of the habit.’

The Irish clergy were noted for the familial character of their profession. In 1250 the Bishop of Ossory complained to the Pope about hereditary succession to the parishes of his diocese. Decrees from the primate of Armagh (who was always from the Pale, a foreigner or an Englishman) and from various provincial synods in the fifteenth century had little effect. In 1546 a visitation of the rural deanery of Tullaghoge, co. Tyrone, revealed some of the clergy as ‘concubinary’. Mahon, son of Bishop Turlough O’Brien of Killaloe (1483–1526), became Bishop of Kilmacduagh (1503–32) and married a cousin. Their son, Turlough, became Bishop of Killaloe (1556–69) like his grandfather, and like his father also married a cousin, a daughter of the first Earl of Thomond.