Sian Griffiths reports on the mystery surrounding the failure of a respected Muslim historian, Ayesha Jalal, to secure tenure at one of America's leading universities. Original", "very very good", "startingly revisionist", "outstanding", "incomparable", "one of the most productive, respected and influential scholars of modern South Asia in the world." A selection from a flurry of praise heaped by academics on the scholarship of young Muslim historian Ayesha Jalal in the past few months.

Columbia University's history department has twice voted to give Jalal a coveted tenured position in its faculty, a roll-call of academe's stars has lobbied and written letters on her behalf, including Harvard economist Amartya Sen, Columbia's own British-born David Cannadine, the founder of subaltern studies, Ranajit Guha and Cambridge's doyen of South Asian studies, Chris Bayly. Yet, dressed in a dramatic pink shalwar kameez, nervously smoking in a friend's London flat, she is now contemplating a law suit against the university. Why?

Her case has, she says, all the hallmarks of discrimination. Reluctant to label herself a victim, she is nevertheless a woman - and a revisionist scholar to boot. Arrayed against her are all the usual problems - with the now added difficulty that Columbia's administrators having refused her application for a permanent academic position, her options are limited. She cannot, she says, return to Pakistan to write her controversial explorations of South Asian history.

For Jalal's work - with its questioning of myths about the origin of the Islamic Republic of Pakistan; its dismantling of the categories "Hindu" and "Muslim" and their underpinning religious differences; its forthcoming attempts to argue for a Bill of Rights for Indians in the face of Islamic law - is, at the least, risky.

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Her first, and best-known, book, The Sole Spokesman, suggests that Mohammad Ali Jinnah, who led the demand for independent Muslim states in northwestern and northeastern India after the collapse of the Raj, did not necessarily intend the result to be the Partition of India. He might have preferred a confederal solution. It is a thesis not calculated to please Pakistanis, who hail Jinnah as the father of their nation. Even more disagreeable to fundamentalists is Jalal's contention that religious difference between Muslims and Hindus was not the only factor in Pakistan's formation. "She argues that the very strong Islamic position they have in Pakistan at the moment is a consequence rather than a cause of the development of India," explains Bayly, of St Catharine's College, Cambridge.

Jalal herself says that her books have met with a mixed reception in India and Pakistan. Scholars have enthused; politicians have raised eyebrows. "I got away with the first - there were rumblings. With the second - about events leading up to the 1958 imposition of martial rule in Pakistan - I was lucky in that military rule ended as it was published. English is so limited there and the books have not yet been translated into Urdu.

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"I come from a country which happens to be Pakistan, where there is no critical academic life," she adds quietly. "I cannot teach at the University of the Punjab. Pakistan's education system is in the doldrums. I am constantly calling into question orthodoxies so I am not going to be popular back home. It does not take long to have you locked up. I have not been locked up because I am in the West."

She adds, wistfully: "I ended up with these handicaps - the fact that I am different. I wear these clothes. My nationality is different. I also happen to belong to a religion which is Islam, a very problematic religion which, now that communism has collapsed, has become the new whipping boy of the West."

Jalal is naturally perplexed about why an ad hoc committee of the university, instead of, as expected, endorsing the history faculty's recommendation that she be promoted, voted to overturn it. The vote was taken last June and brought to an end two long years of waiting for Jalal, who is still employed as an associate professor of history at Columbia, where she is supervising five doctoral students.

Before that definitive June meeting she had surmounted all the normal obstacles of the tenure procedure. First there was an internal review of her application within the department. Twenty-three votes were cast; 22 for Jalal. Then external reviewers of her work were sought. Only two negative letters were received. The rest - 18 or so - were effusively complimentary. All this was undone by the five-person ad hoc committee that turned her down flat, leaving members of the history department bemused and infuriated.

When the academic year started in September the historians passed a resolution deploring Jalal's rejection and demanding a reassessment. Letters of protest flooded in to the office of provost Jonathan Cole from scholars working across the world in the field of South Asian studies. One, from Ranajit Guha, conveys the flavour. Guha, now at the Australian National University, writes: "[Jalal] is one of the outstanding academics writing on South Asian history today and incomparable, even amongst them, in the scope and depth of her scholarship [on] Pakistan and the politics of inter-communal relationships in the subcontinent." Columbia has, however, refused to reconsider and is standing by its decision.

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Jalal knows that objections were raised at the ad hoc committee meeting to her third book, Democracy and Authoritarianism in South Asia, which explores why Pakistan and India developed along different political routes despite having a common colonial legacy. Some committee members also raised queries about a paper she submitted entitled "Exploding Communalism: the politics of Muslim identity in South Asia", which draws from her forthcoming fourth book, which, boldly, brings her exploration of Muslim identity right up to the present day.

But fellow scholars struggle to find academic reasons for denying her a post. David Taylor at the School of Oriental and African Studies in London says: "She should have got tenure. I was staggered when I heard she had not. She is an abrasive person, but that is not a reason to deny someone tenure."

Bayly comments: "It is extremely important to remember that the Columbia history department has twice voted that she should be given tenure. This has been suppressed at the university level for reasons which are not at all clear."

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Explanation is not forthcoming from the university, which regards the tenure procedure as confidential. Stephen Rittenberg, vice provost for academic administration, says only: "We conducted a tenure review and the decision was that she did not have the qualifications needed for tenure." He added that the majority of applications that are supported by the department nominating a candidate (the first stage of the tenure process) are approved at the second stage, but that "10 to 15 per cent are turned down at ad hoc level". In the past disappointed candidates have sued, but to date, says Rittenberg, none has been successful.

Jalal is determined. She has found herself a lawyer willing to pursue a case alleging discrimination against Columbia. She knows that legal challenges have been mounted before and that such disputes are costly and bruising. But she feels she has no other option. South Asian history is a small field, jobs are few and far between. For Jalal, with a doctorate from Cambridge, previous fellowships and temporary teaching posts at Harvard, the University of Wisconsin, Madison and Tufts, Columbia is her most recent stop in her bid to establish a glittering academic career in the West.

"I find it really distressing when colleagues I started with are all now settled and I still haven't got a permanent job. I have worked so hard. I can understand people do not like all your work. But what criteria determine how people get jobs in this field?" More worrying perhaps - as she herself says - her work actually might make a difference to the vexed politics of the sub-continent where Hindus and Muslims are at each other's throats, where Islamic law, in Pakistan, denies women fundamental human rights and where non-Muslim groups, such as the Ahmadis, are already being outlawed. Jalal's research is important, apart from its historical accuracy, because it challenges the categories that underpin such ways of thinking, allowing for the possibility of forging some kind of path, perhaps drawing on democratic philosophies, which could accommodate ethnic and religious differences.

Indeed, such differences cannot be confined to the sub-continent. America and Europe, too, are faced with how to manage the kinds of arguments which disrupt multi-ethnic societies. Even on Columbia's New York campus Jalal found herself embroiled in a dispute spanning India and the West when she, along with a group of other academics, opposed a multi-million dollar gift to the university by S. P. Hinduja, a notable Hindu businessman. Hinduja gave the money to set up an institute for Indic studies in memory of his son.

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With ethnic and religious conflicts erupting across the world, the need to appoint scholars who can offer insights into and explanations for such disturbances seems overwhelmingly obvious. As she concludes, and many in the field have agreed: "It is a little sad that Muslims who could act as a bridge and establish a dialogue between Asia and the West are being denied jobs they are entitled to on merit."