Controversies surrounding Ledwith's appointment as President of St Patrick's College, Maynooth in 1985 were discussed in the national media in 2002. It emerged that in 1983–84 Fr Gerard McGinnity, then Senior Dean of Maynooth, complained about Ledwith to seven bishops including the Bishop of Ferns, Dr Brendan Comiskey, who was championing Ledwith's appointment, Cardinal Tomás Ó Fiaich and Bishop Cahal Daly. The 2005 Ferns Report said that the complaints related to alleged homosexual "orientation and propensity" rather than any improper conduct. The then Bishop of Galway, Dr Eamon Casey, conducted a private investigation, and as no seminarian came forward to make a complaint, the matter was dropped. In the immediate aftermath, as McGinnity's position was deemed untenable, he was required to leave the College, and Dr Ledwith's appointment was confirmed.