If this is the season for confession in the field of religion and politics, I have a confession to make. As a biographer, I did not get Tony Blair's Roman Catholicism. Like many other people, I made the mistake of assuming that he was like me. Not that I am a Christian; but I am, as they say in Northern Ireland, a Protestant atheist. The God I don't believe in is a New Testament God who has little time for the Pope.

I remember one meeting I had with Blair when I asked about the speculation that he would convert to Catholicism when he stopped being prime minister. He said something dismissive, which I took to mean that the speculation was wrong. I tried to define the nature of his faith by describing him as an ecumenical Christian. He agreed and smiled sweetly.

So when, a few months before he stood down from office, I learnt from a reliable source that he did indeed intend to convert, I felt a familiar sense of disappointment. It was a feeling I had when we got to 1685 in A-level History, and Charles II, a clever and subtle politician, converted to Catholicism on his deathbed. After all that! The English Reformation; the Civil War; the attempt to exclude Catholics from the succession. After everything, it turned out that he was working for the other side all along.

The disappointment is not, in Blair's case, because I think that Papism is a foreign plot to rob this country of its national identity, but because I do not understand it.

Nor did the mostly "godless lot" who worked for him as prime minister, although it did not bother them. Once, I was talking about his religion to one of them, who said, "Oh, you mean all that stuff?" and mimed prayer out of his eye-line, with him in the room. The implication was that it was one of those foibles up with which they simply had to put. Alastair Campbell took a similar view, which led to one of his most famously misunderstood statements.

"Is he on God?" he asked, overhearing an American journalist ask about religion in the middle of a long interview. "We don't do God," he said, lightly, allowing his boss to deflect a line of inquiry that had proved unhelpful in the past.

It had been unhelpful a spin doctor's favourite word at Easter 1996, when Blair was persuaded by Matthew d'Ancona to write an article for The Sunday Telegraph that said, in effect, that Conservatives are unChristian.

Two other pronouncements on his faith got Blair into trouble. The first, which I reported in my biography, was his letter to the late Basil Hume, in which he accepted the Cardinal's ruling that he should not take Catholic communion but added: "I wonder what Jesus would have made of it." There was a cosmic arrogance to it, but especially for Protestant atheists there was much in his spirit to admire.

The second was his aside to d'Ancona in 1996, as they were discussing the Sunday Telegraph article. "Jesus was a moderniser," he said. Factually, it was an uncontroversial statement, and this time the cosmic arrogance appeared to be more accidental.

Nor did I find it hard to understand his wife's Catholicism. She is a Catholic by upbringing rather than a convert. She has no time for the Pope's teaching on birth control or women priests, and like her moderniser husband regards the Church and the Labour Party as comparable organisations.

In her contribution to a book called Why I am Still a Catholic two years ago, she wrote: "I have been taught that you should stay and try to change things. It's like the Labour Party in the early 1980s. I wasn't happy with the way it was going so I tried to help change it from within."

Now, however, Blair has been received into the Roman Catholic Church by Cardinal Cormac Murphy O'Connor. Well, I can see why he wants to take part fully in the services attended by Cherie and seven-year-old Leo. And I can see why he, and the rest of us, would enjoy the offence given to the fundamentalists within.

Most notable was the warm and welcoming embrace offered by John Smeaton, the director of the Society for the Protection of Unborn Children: "We need to hear a full repudiation from him. Without one, having Blair as a Catholic is like having a vegetarian in a meat-eating club." (Surely he meant a meat-eater in a vegetarian club?)

However, there is a serious end-user licence to joining the Catholic Church. It is not like clicking Accept on a software download; Blair had to read all the terms and conditions and mean it when he said, "I Agree".

I know Cherie does not agree with the Pope, but it is different when you choose to switch your religious affiliation. This is a Pope, we should remember, who earlier this month offered indulgences a discount on time spent in Purgatory for pilgrims visiting the shrine at Lourdes. A special limited offer, available for only 12 months from 8 December this year.

Not that the Church of England is theologically straightforward, as anyone will know who heard the Archbishop of Canterbury trying to explain on the radio why the three kings are a "legend" but the Virgin Birth is true in a "deeper sense".

But what I cannot understand is how subscribing to one sect with a claim to absolute truth can help to bring religions together. Yet that is the mission of the Tony Blair Faith Foundation, to be launched in the new year. Many of its staff, including Ruth Turner, who was Blair's minder at No 10, are Catholics.

The question for a biographer, though, is whether, retrospectively, any of this matters. Blair's government, as Smeaton testifies, was liberal on abortion. The two Catholic fusses of Blair's final months in office were mere politics: Alan Johnson made an error in trying to change Catholic schools' admissions policies without first preparing the ground; and Blair brokered a compromise with the Catholic agencies on gay adoption that was simply pragmatic.

It remains true that, at no point in his time as Prime Minister, does one need to refer to Blair's religion in order to explain his motives and actions.

There are, also, always realms of the inaccessible in the mind of the subject of any biography. Anyone trying to understand Gordon Brown comes across similar unknowability, albeit of a rather different kind. Tom Bower, Brown's hostile biographer, wrote earlier this month that, "on arriving at Edinburgh University, Brown described himself as an atheist". In 1994, Brown joined the Christian Socialist Movement, of which the then leader of the Labour Party, John Smith, was the leading member. Whether this was a spiritual journey or an electoral one is as obscure as Blair's view of transubstantiation.

At least Nick Clegg, the new Liberal Democrat leader, gave a straight answer that, whatever you think of it, poses no obstacle to understanding. Do you believe in God, he was asked in a rapid-fire radio interview. "No." Perhaps I should write a biography of him.