The current row over gender in Portadown, where a Presbyterian minister refused to allow a female cleric into his pulpit on grounds of " conscience" is making headlines, for all the wrong reasons. However, it is a good example of a large Church grappling with major changes. The Rev Stafford Carson of the First Portadown Presbyterian Church said that " in conscience " according to Scripture he could not allow the Rev Christina Bradley of Armagh Road Presbyterian Church to preach from his pulpit during a joint service on Christmas Day.
This row strikes at the heart of women's rights and of freedom of conscience. Though both ministers have agreed to work harder at finding a solution, Mrs Bradley has said that the situation "saddens me and puzzles me. These are views that are not incompatible with the laws of the land".
Meanwhile, the Moderator, the Rt Rev Dr John Finlay, is trying "to square the circle." He said on radio that the Church's stance on " gender equality" is clear but also underlined the right of a male cleric "in conscience" to bar a women from his pulpit. This situation seems contrary not only to law but to common sense, and unless the Church gives a clear lead on backing women in the pulpit, it will try in vain to "square the circle" while a sceptical world looks on.
The Presbyterians are also facing other issues, including the election of a new moderator next month.
In the past, the 21 presbyteries met to choose a moderator from a list that seemed to evolve at the last moment from thin air. This year, in an attempt to provide more transparency, the names are being listed in advance and this will be welcomed by the rank and file.
The Free Presbyterian Church also faces the election of a new moderator to succeed the Rev Dr Ian Paisley, who has held the position for well over 50 years. Observers have suggested that he volunteered to stand down to avoid a split because some Church members disapproved of his decision the share power with Sinn Fein.
However there may be other factors at play, including the increasing burden on Dr Paisley as First Minister.
Senior sources within the Church have suggested that the Free Presbyterians may decide to elect a moderator for only one or two years - roughly in line with the Presbyterians and Methodists.
The Catholics have no such problems, and their senior clergy hold office virtually for a lifetime, but usually not beyond the retiring age of 75 for a bishop.
However the Bishop of Down and Connor Dr Patrick Walsh, who formally offered his resignation nearly two years ago, remains in office. An announcement has been expected by clergy and laity for some time, but to no avail.
One of the major challenges facing the Catholic Church worldwide, as well as a drop in vocations, is the continuing shadow cast by the scandal of clerical sexual abuse.
In America, the Catholic Church is estimated to have paid out $$2bn to victims, and the Pope has already instructed Catholics to pray "in perpetuity" to cleanse the Church of paedophile clergy.
The latest figures show that around 100 allegations of such abuse were made in Ireland in the 40 years from 1962, and that 21 priests were involved.
Meanwhile, the Anglican Communion, including the Church of Ireland, has its own problems, including how to deal with same-sex relationships.
This issue threatens to split the Church world-wide and will be a top priority at this year's Lambeth conference.
The challenges for the Irish Churches have changed dramatically as the peace process beds in.
The relatively clear-cut challenge of opposing violence has been replaced by the complexities of gender, sexual orientation and other issues. How they face up to these will be their test of credibility in an increasingly secular world.
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