The beautiful chapels ensure that religion is literally built into the fabric of most Oxbridge colleges, regardless of whether anyone actually attends evensong. But what about the study of theology?

"There has long been a fear in theological circles that they will be squeezed out," explains Andrew Louth, professor in the department of theology and religion at Durham University, "and this was strengthened with the foundation of universities that, by their charters, allow no place for theology or religious studies. Liverpool and York are the obvious examples, though the most ancient is University College London (1826). When I took up my first university post 37 years ago in Oxford, the theological faculty already had a long history of feeling embattled."

A major turning point had come just before that, in 1967, when Ninian Smart essentially "repackaged" theology as a dispassionate form of academic inquiry and established the first British department of religious studies at Lancaster University. His high media profile and interest in comparative religion led him to become something of a globetrotter, to the irritation of many colleagues. Hence the joke: "What is the difference between God and Ninian Smart? God is everywhere, Ninian Smart is everywhere except Lancaster."

In 1992, by contrast, theology got an unexpected and totally accidental boost from the reforms that created the "new universities", since many were originally religious foundations and brought with them a commitment to the discipline. Yet many questions remain about theology's place within the modern university.

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The stakes have been raised by the recent flood of anti-God polemics, many by academics such as Daniel Dennett, A. C. Grayling, Michel Onfray and Lewis Wolpert. None has had the eloquence or impact of Richard Dawkins' The God Delusion.

This, of course, is a ferocious assault on every aspect of religion, comes close to equating religious education with child abuse and promotes an unashamed crusade for atheism. "If this book works as I intend, religious readers who open it will be atheists when they put it down," writes Dawkins.

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The God Delusion also includes a story about the astronomer Martin Rees referring to a couple of "ultimate questions" as lying "beyond science", in "the province of philosophers and theologians". "I would prefer to say," writes Dawkins, "that if indeed they lie beyond science, they most certainly lie beyond the province of theologians as well ... I am tempted to go further and wonder in what possible sense theologians can be said to have a province ... I have yet to see any good reason to suppose that theology (as opposed to biblical history, literature, etc) is a subject at all."

Theologians have legitimate concerns that Dawkins would like to do them all out of a job. So do they see him and fellow militant atheists as a threat? Several have responded with full-length books, arguing that religion is not as bad as Dawkins says or suggesting ways for science and religion to get along out in the world. But there is also the more parochial question of whether they can coexist within British universities. And, since no one wants to expel the scientists, this really comes down to the status of theology.

Is it largely designed to offer vocational training for clerics? Is it a legitimate academic discipline whose subject matter (like, say, psychoanalysis) just happens to be deeply significant to some people and totally vacuous to others? Should it look back to its medieval heyday as "queen of the sciences" or act as a subversive force, in creative tension with the values of the rest of the academy and the wider society beyond? And what are theologians doing to combat the religious homophobia and squeamishness about sex that people such as Dawkins claim have blighted many lives?

Dawkins' own base at New College, Oxford, seems a good place to start. He recognises the irony that it was founded in 1379 by the Bishop of Winchester, William of Wykeham, as "a great chantry to make intercession for the repose of his soul". Wykeham provided for the service of the chapel by ten chaplains, three clerks and 16 choristers, and he ordered that they alone were to be retained if the college's income failed. There are now just two symbolic prayers for Wykeham's soul per year, and a single chaplain, Canon Jane Shaw.

What is it like to be the chaplain at what some might see as the headquarters of an atheist crusade? Do Shaw and Dawkins glare at each other over lunch at High Table?

Not at all, says Shaw. "New College is far from being the headquarters of an atheist crusade. No fellow would make the college the HQ of their academic or personal interests in a way that would be discourteous to another fellow. Being chaplain of the college, where a famous atheist of a particular scientific bent happens to be a fellow, is just fine ... He and I get on well and have amenable conversations over lunch, but this is what we would each expect of a colleague."

Other theologians feel that Dawkins has missed the point, arguing that their subject could and should be an objective discipline. As Esther McIntosh, lecturer in religion, gender and ethics at the University of Leeds, puts it: "Academic theologians ought to be open-minded about religion, able to be honest about the damage that religion can and does do, while also seeking to analyse the positive benefits of religion, if there are any."

Just as one can study Jungian psychology or Marxist politics without being a Jungian or a Marxist, she continues, "it is equally possible to teach and research theology without being religious. It is possible to consider the arguments on their own terms. Dawkins has misunderstood the discipline and assumed that it requires a faith stance."

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Oliver Davies, professor of Christian doctrine at King's College London, agrees that his job as an academic is not about "doing theology" but about helping students "understand theology". And this, of course, could help them to understand many other crucial contemporary challenges.

"Recruitment is buoyant at the moment because people see the influence of religions in our societies - for better or for worse - and want to understand them," Davies says.

"Universities offer training in manipulating (theological) counters that are empty to those who don't buy into them but that are nevertheless some of the most formative factors in the continuing evolution of the modern world. Looking at the US, China, India and the Middle East suggests that religion will play a critical role in different ways in our global futures."

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Davies also sees a vital public role for theologians. Historically, he explains, it was they "who have facilitated the ways in which religious communities have reconciled their faith traditions with changes taking place in the world about them". Today, we urgently need "a modern generation of Islamic theologians" to engage with "the social topics in which the tension between religious tradition and secularism comes to the fore".

"Public dress, the equality of women, use of leisure time, technology and its uses, as well as the more fundamental issues of revelation and state law, come to mind. It is in departments of theology that an environment can most easily be constructed in which Muslims can do this kind of thinking," he says.

Other theologians are more alarmed. Andrew Louth sees the arguments of people such as Dawkins as a threat not just to theology departments but to "the values implicit in the university from the beginning - values rooted as much in classical culture as in Christian culture". Today, he argues, we are witnessing the emergence of "a society that has no access to values beyond immediate satisfaction, and in this context the idea that science has the answer to everything seems more and more plausible, because what science can't provide - roughly the humane values we used to take for granted - has, as it were, dropped beyond the horizon of consciousness. The very shrillness of Dawkins et al might actually remind people that their claims can't be true, because they seem to be arguing so strongly against something that, therefore, must be there, despite the lack of purchase it has on our consciousness."

Yet, while many theologians argue that their subject is a legitimate discipline that should take its place alongside others in the modern secular academy, others believe this is a betrayal of its essence. Gavin D'Costa, professor in Christian theology at the University of Bristol, recently delivered a talk where he suggested that theology "needs to be prised free of its subservience to the Enlightenment model of the university" and "argue for a different type of university that would support the proper way of studying theology".

The ideal of "religious studies" established by people such as Ninian Smart, complains D'Costa, "proposed a method that definitely and distinctively should not and could not involve faith as its starting point" and abandoned the "traditioned form of exegesis, which also invoked the aid of the Holy Spirit". The real intellectual threat to the discipline, he argues, comes not from vociferous atheists but from "theologians who don't do theology properly: ecclesiastically".

D'Costa is well aware that, in the current climate, "for theologians to argue for alternative universities might almost seem tragicomedy or farce". But he clearly believes that his colleagues' form of "academic theology" amounts to selling out and that theologians ought instead to act as "subversives within the secular university".

Something of the ways in which theology can be subversive are illuminated by Gerard Loughlin, professor in the department of religion and theology at Durham University. He attributes some of the success of Dawkins' book to the failures of the churches, which "have arguably retreated from presenting faith as a rational venture and allowed themselves to worry away at sexual morality".

On the latter issue, Loughlin's own views couldn't be clearer: "Sex is given for many things - fun, companionship, children - but ultimately and fundamentally it is given for knowing God (there is a reason for the tradition's use of sexual imagery for thinking about the soul's union with the divine)."

Loughlin recently edited a book, Queer Theology: Rethinking the Western Body (Blackwell), which includes essays by Shaw, D'Costa and a number of other British academics. This, he explains in the introduction, obviously includes a critique of Christian homophobia, of churches "refusing to see, let alone sanction, the same-sex bonds that are everywhere present in their midst". But it goes further: "As so often, the very thing denied is affirmed and celebrated at the level of the Christian symbolic - in the Church's imaginary life, in her stories and songs, parables and prayers. This is one of the queerest things about the Christian Church; that it celebrates in its symbols what it denies to its members." One might say the same, of course, about paintings of figures such as St Sebastian.

Queer theology, Loughlin confirms, "is trying to subvert a great deal of what is taken for granted about Christianity by people both within and outside the churches ... But for me much of this unsettling is already there in the most orthodox passages of theology, so that queer theology is about releasing what is already present."

Dawkins, it is fair to say, detests theology but has no deep interest in the subject. For anyone who actually goes out to talk to theologians, the discipline seems to be in rude health, stimulating, surprising - and surviving very well under atheist assault.