Eamon Duffy secured his historical reputation with a great and eloquent book, The Stripping of the Altars, listening to voices that others had missed. Thanks to that and his later book, Fires of Faith, we can reassess both pre-reformation religion and the version of Catholicism that Queen Mary and her Archbishop of Canterbury, Cardinal Reginald Pole, rebuilt after Protestant mayhem. Now Duffy gathers up a number of essays pushing further the same project.

Much of this book works; a significant amount doesn't; none of it is dull. It opens with polemical surveys of how English reformation history has been written and Protestant English identity created, and it moves on to delicious though elegiac studies of how English parish life was transformed in the Tudor age. There are insightful and empathetic portraits of two Catholic prelates. First is the gaunt but hospitable Bishop John Fisher, a great theologian and a martyr for papal obedience at the hands of Henry VIII. Then we meet the refined, aristocratic and enigmatic Cardinal Pole, who despite knowing that Martin Luther was right in his theology of justification by faith alone, created martyrs in two contrary senses, resurrecting the reputations of Fisher and Thomas More, while enthusiastically hounding leading Protestant clergy to death at the stake; Thomas Cranmer was the most exalted victim. Duffy is very good at seeing the realities of Mary Tudor's regime, for good or ill: he even mentions that she burned quite a lot of Protestants.

The last section returns to "voices", those who opposed the developing reformation. They frequently did so with effective pointed wit, and always with a passionate sense of tragedy. Some, as Duffy points out, did not defy the new Elizabethan establishment, and paradoxically seeded their attitudes inside the reformation Church of England, which has generally been better at being rueful about its past mistakes than other churches one could name.

Reading through this pageant with much enjoyment, I kept applying the brakes with a "Yes, but " Repeatedly I noticed assertions pushing evidence beyond what is justified in the interests of making a tidy and cogent case. For instance, it may be true, as Duffy says, that it was only in the late 1650s that Mary Tudor was called "Bloody Mary" in print, but a century before, Edwin Sandys, vice-chancellor of Cambridge and Elizabethan Protestant bishop, was fond of calling her just that; only propriety during the reign of Mary's half-sister prevented more widespread public abuse. In Duffy's account of the grand and hauntingly beautiful parish church of Salle in Norfolk, he wants a particular clergyman, Roger Townsend, rector of Salle, not to be a pioneer Protestant at all. So he devotes three pages to explaining away all the evidence that Townsend was indeed a pioneer Protestant, while missing the significance of one killer fact he actually cites: Townsend left a big pot of money for commemorative sermons by one of his clerical neighbours, Robert Nicolles, who just happened to be one of Archbishop Cranmer's chaplains and one of the most aggressive Protestants in Henry VIII's Norfolk.

Of wider importance is Duffy's take on the great East Anglian popular commotions of 1549, now known as Kett's Rebellion. He is patently uneasy with a heap of evidence that the mood and rhetoric of the crowds involved were pro-reformation; that's just too many Protestants for mid-Tudor England, who on Duffy's reading shouldn't be there. So he seizes with relief on the fact that when one village contingent marched off to Robert Kett's great camp at Norwich, they carried with them the banner from their village church. That does look a rather pre-reformation or even anti-reformation thing to do, until you realise that is precisely what a lot of villagers had done in the great German popular uprisings of 1525, inspired by Martin Luther's revolution against the Pope.

Duffy should consider the significance of the next two upheavals of Tudor England: Mary Tudor's coup d'état against Queen Jane Grey in 1553 and Sir Thomas Wyatt's rebellion against Queen Mary six months later. Neither Mary nor Wyatt laid any emphasis on the religious cause that really excited them  Roman Catholicism in Mary's case, Protestantism in Wyatt's. Instead Mary talked about her claim to the throne as Henry VIII's daughter, Wyatt tried to arouse English fear of foreigners. Why was that? Because they both realised that they would alienate too many potential supporters across the religious divide if they talked about religion; they knew that England was already deeply split between Catholics and Protestants. That is the reality of mid-Tudor England.

The last sentences in the book are frankly silly. Playing with recent assertions that William Shakespeare was a Roman Catholic, Duffy asserts on the strength of a single famous but elusive phrase in one Shakespeare sonnet about "bare ruin'd quiers" that "In the mind and mouth of the most illustrious of all Elizabethans, the Tudor religious revolutions had elicited not even the most equivocal of endorsements". This is said of the playwright who systematically, though with his usual subtlety, turned Henry V, that most popish of medieval English kings, into a Protestant avant la lettre, who cast Archbishop Cranmer in the role of prophet of a golden Elizabethan age in his collaborative play Henry VIII, who used the craggily Calvinist Geneva Bible as much if not more than any other biblical translation, and all through his career, fruitfully (though with increasing discrimination) drew on the classic Protestant historical narratives created by John Foxe.

That illustrates the besetting fault of this collection. You wouldn't expect Duffy to write a book about Protestants, because he is writing a book about Catholics. But to write a really effective book about Catholics, one has to listen in a balanced fashion to voices on the other side. There are a number of fine leading historians in this country who are Catholics, but you wouldn't know it when they write about the reformation: they are historians of Tudor England who happen to be Catholics. At times here, Duffy ceases to be a Tudor historian who is a Catholic, and becomes a Catholic historian. That will please many, but it's a shame: almost as bad as being a Protestant historian, rather than an historian who is a Protestant.

Just for the sake of balance, let me tell you a true story which I don't recall figuring in Duffy's various accounts of Mary Tudor's church (apologies if it does). In 1566, Elizabeth I's archbishop of Canterbury, Matthew Parker, was disconcerted to receive a bill from the bailiffs of the city of Oxford. They were still owed £43 out of the £63 that was their expenditure for guarding and burning Hugh Latimer, Nicholas Ridley and Thomas Cranmer, back in Mary's reign. Mary's government added meanness to its brutality, and had not paid up. "The case is miserable, the debt is just," the Puritan president of Magdalen College wrote in perplexity to the archbishop. So Parker, feeling that it was only fair, had a whip-round among his fellow Protestant bishops to pay for the expenses of burning England's most famous Protestant martyrs. I wonder if any counter-reformation bishops would have reimbursed damnable heretics, had they presented that sort of bill.

 Diarmaid MacCulloch's A History of Christianity: The First Three Thousand Years is published by Allen Lane.