As apologies go, this one will be historic. Tomorrow is billed by the Vatican as the Day of Forgiveness when the Pope apologises for the sins of the church over the last millennium. No one knows yet what he is going to say, but it is bound to be snappier than the 30-page statement on the subject issued this week by the International Theological Commission.

The Pope has gone through this before: he has either asked forgiveness from assorted groups who may have had a raw deal from the church - his letter to women, say - or expressed regret for historical events in which the church was implicated. Of these, the one that seems most personal is in respect of the Jews, a community with which he grew up and where he had friends - and whose fate during the war is bound up with his own experience.

And as a Pope who takes the millennium-jubilee year as the high point of his pontificate, he also takes to heart the notion that the jubilee has to involve a purification of the collective memory of the church from the "counter-witness and scandal" of the last millennium. An awful lot to purify, you might think.

This is all very moving, but the real danger is that this whole exercise will become an attempt to project the moral sensibilities of the 21st century on to the past, that other country whose people didn't see the world as we do. For instance, during one of his previous apologies the Pope called to mind "the lack of discernment by many Christians in situations where basic human rights were violated". A millennium ago you couldn't talk about basic human rights because people didn't think in the terms of the American constitution.

This is not at all to say that morality is relative. The notion that innocent human life is sacrosanct or that stealing is wrong or forgiving enemies a duty is always with us. But it does mean that moral sensibilities change. The revulsion most of us feel for the death penalty for murderers would have seemed at least eccentric a century ago.

This very obvious point is acknowledged by the International Theological Commission. "Can today's consciences be assigned `guilt' for isolated historical phenomena like the Crusades or the Inquisition?" it asks, "Isn't it a bit too easy to judge people of the past by the conscience of today . . . almost as if moral conscience were not situated in time?"

Well, quite so.

Anyway, who is doing the apologising, and for whom? The Pope, for the sins of individual Christians or for the acts of the institutional church? The document on forgiveness talks, as does the Pope, about the sins of the sons and daughters of the church. But what about the actions of the institutional church? Do we get round that by separating the institution from the magisterium, the teaching authority?

Take the knottiest problems, the Crusades and the Inquisition. The Crusades were initiated by a pope; sustained by almost every pope up to the 16th century; championed by countless saints like Bernard of Clairvaux, Thomas Aquinas and Francis of Assisi; and promoted by the canons of five general councils. You can apologise for excesses committed by Crusaders - some were condemned at the time - but for the whole project? How could the Pope do so, without doing violence to the integrity of other popes?

Urban II launched the Crusades in 1098 for two purposes, to help the Orthodox Christians whose emperor had begged him for assistance against encroaching Islam, and to reclaim the holy places, which were seen in the terms of the time as the patrimony of Christ. Indeed, earlier in the 11th century the holy places had been desecrated by a rather unhinged sultan, and Jerusalem had indescribable emotional appeal as a place of penitential pilgrimage: its reclamation seemed like an indisputably loving act.

We might balk at the notion of the armed pilgrimage and have problems with the idea of Christ's patrimony, but the fact is that that is how contemporaries saw it.

What about forced conversions, violence against heretics, the Inquisition? The church quite explicitly condemned forced conversion of pagans, though it happened in practice, but the use of violence against heretics was sanctioned by the church; indeed, the intellectual justification was provided by St Augustine.

As for the Inquisition, it was established in 1233 by Pope Gregory IX as an extra-judicial process for dealing with an unappealing sect, the Cathars, and although the Inquisition never actually killed anyone (it handed over known heretics to the secular government to be dealt with) it is difficult for us to appreciate the distinction.

There is one way out of all this. At the seminar of historians summoned by the Vatican to discuss the Inquisition, the distinguished Jewish historian, Carlo Ginsberg, said forcefully that any talk of asking pardon for the past was simply unreal and he would rather hear the Pope say simply that he was ashamed of the past, rather that asking for easy absolution.

That may be the Pope's best option tomorrow: to express his own shame for Christian iniquities, express a collective willingness to sin no more, and just leave it at that.

Melanie McDonagh is a freelance journalist