Government whips are right to be scared in the run-up to the autumn vote on tuition fees. Philip Cowley charts the swelling ranks of rebel MPs.

Until recently, it was the political science equivalent of stamp collecting. The discovery that I spent my life researching the way MPs voted was a guaranteed conversation stopper at parties, the cue for glazed eyes and the sudden discovery of someone much more interesting on the other side of the room. Who cared?

Then, seemingly out of nowhere, came the two enormous backbench revolts over Iraq - and suddenly lots of people cared. In the first, in February, 122 MPs voted against their party whip; in March, the figure was 139. These were the largest rebellions against the whip by government MPs since the beginning of modern British politics, easily surpassing the previous records: the 110 Labour MPs who rebelled over agricultural rent reform in 1975; or the 95 Conservatives who voted against the post-Dunblane firearms legislation. To find a bigger rebellion, you have to go back to the Corn Laws.

They were followed by similar opposition over foundation hospitals. May's was the largest at a bill's second reading for almost two decades, July's reduced the government's majority to just 35, the narrowest it has been since 1997 as a result of a rebellion.

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But rather than coming out of the blue, these revolts are merely the latest evidence of increasingly rebellious behaviour on the back benches. As well as Iraq and foundation hospitals, the past two years have also seen large votes against the government line over faith schools, anti-terrorism legislation, jury trials, immigration and asylum, and community health councils. The previous full session of Parliament (2001-02) was the most rebellious first session of any Labour administration. The idea that the whips face an acquiescent parliamentary party is simply laughable.

And when Parliament resumes in September, the issue of top-up fees will be lying in wait for the government. Three separate early-day motions against top-up fees have been signed by as many as 139 Labour MPs. Do not be fooled by the small rebellion over the issue in June. That was on a Liberal Democrat motion, and most Labour MPs hate voting for anything proposed by the Lib Dems. Much more worrying for the whips were all the MPs who simply stayed away. If the government scrapes a narrow victory in the vote, it will provoke yet more talk about the West Lothian question and the inequity of Scottish MPs helping enact legislation for the English that won't apply back home. But there are plenty of Labour MPs who think that this could be the issue that produces this government's first parliamentary defeat.

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Either way, expect a whopper.

The irony in all of this is that after their election in 1997, Labour MPs acquired a reputation for excessive cohesion, excessive loyalty and a lack of backbone. They were timid, gutless, sycophantic and cowardly. Writing in the New Statesman after the first Iraq revolt, the comedian Mark Thomas said that he "didn't realise there were 122 spines in the Parliamentary Labour Party". So where has it all come from?

In fact, the spinelessness of Labour's MPs was always a myth. A year ago, hawking my last book around TV and radio studios in a desperate (and ultimately futile) attempt to flog a few extra copies, I grew used to the looks of sheer incredulity that greeted any suggestion that Labour MPs were something other than sheep. Before one interview, I spent an hour briefing a local TV station, hammering home the message that "they" were not sheep.

When I got to the studio, I found that they had prepared a graphic to accompany the interview filled with pictures of - you've guessed it - sheep.

Yet the previous Parliament saw almost half the backbenchers vote against their whip. There were plenty of revolts that were, on average, larger than in every Parliament between 1945 and 1966, larger than those under Edward Heath between 1970 and 1974, and larger than those during the four consecutive Conservative governments between 1979 and 1997. For "poodles", Labour MPs could bark loudly when provoked - and a lot louder than Conservative MPs used to.

And the natives are becoming increasingly restless. At its halfway point, the current Parliament has already seen more rebellions than the whole of the last one. Part of the explanation for this increase is obvious: the back benches now contain more MPs who have personal reasons to be disgruntled with the leadership, including all those who have been sacked from ministerial office or passed over for promotion - what one senior whip called "the dismissed and the disappointed". The former grouping alone now numbers more than 90, of whom Clare Short, Robin Cook and Frank Dobson are merely the most obvious. But as well as this, there are two other explanatory factors that are less commonly appreciated.

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The first is that the self-discipline that was exercised by many Labour MPs for much of the previous Parliament has declined. When first elected to government, lots of Labour MPs, even those on the left, took a conscious decision - motivated in part by the spectre of squabbling Conservatives in the preceding Parliament - not to rebel unless forced to. Faced with a choice of being seen as clones or being seen as disunited, many chose the clones. As time goes on, especially as the Conservatives continue to fail to make any obvious recovery, so the pressure to be self-disciplined has receded. Tony Blair's recent speech to the PLP, in which he appealed to members not to let disunity allow the Conservatives back in, was an (unsuccessful) attempt to reinstall some of that self-discipline.

Last, there's what Tony Benn calls "the ishoos". Even the most independent-minded Labour MPs does not vote against the party just for the hell of it. It takes the right issues to spark revolts. Iraq was just such a trigger. So are many of the pieces of "reformist" legislation that the government is trying to enact. The issue of top-up fees is particularly problematic because it antagonises MPs from heartland seats (who fear that working-class students will be deterred from going to university) and those who hold more middle-class constituencies as a result of the Blairite landslides (and who fear the electoral consequences of hammering their voters).

Faced with this increasingly rebellious party, the government is responding much as all modern governments have done. The conventional view of the whip is that of arm-twister, bully and Machiavelli all rolled into one - as personified by the fictitious Francis Urquhart. But, in reality, the main weapons in the whips' armoury are simply persuasion and negotiation, with the latter used when the former has failed. Despite their reputation as an autocratic government, ministers have since 1997 for the most part been good at heading off potential trouble by sugaring the legislative pill. But as the PLP becomes more rebellious, ever more sugar is needed. The foundation hospital revolts would have been much greater had it not been for a series of concessions offered in the run-up to the votes. There have already been signs of movement over tuition fees, but expect more over the next few months as Alan Johnson and Charles Clarke attempt to buy off enough of the rebels.

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What makes things even worse is that after MPs have rebelled once, it is much easier to do so again. The dangers of recidivism are very real.

Rebelling for the first time is a bit like losing your virginity (although the comparison's not perfect, not least because each division in the House of Commons takes between 12 and 15 minutes). And so, with each rebellion the number of potential rebels for the next grows ever greater.

But perhaps the biggest problem for the government is not what will happen in the next two years, but what will face them after the next election, when Labour (if re-elected) will almost certainly have a smaller majority.

Now that the habit of rebellion has become widespread, governing with a small majority will be very difficult. For precisely this reason, the whips wanted to keep the parliamentary party full of dissent virgins. They have instead ended up with MPs who are increasingly, and dangerously, promiscuous.

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Philip Cowley is a politics lecturer at the University of Nottingham and author of Revolts and Rebellions: Parliamentary Voting under Blair, published by Politico's (?20.00). He has just been given a ?110,000 grant by the Economic and Social Research Council to investigate parliamentary voting in the 2001 Parliament.