The conference vote was a disappointment for Mr Alton's fellow MPs who had hoped to keep him on board by preserving the status quo under which abortion was seen as an issue for personal conscience, not party policy.
However Paddy Ashdown, the Liberal Democrat leader, observed that Mr Alton had played no part in building the new party - a comment which stung Mr Alton and prompted suggestions at Harrogate that he might resign the party whip in the Commons.
Women Liberal Democrats argued that the motion demanding equal access to NHS terminations was not about changing the law but ensuring its fair implementation. But for Mr Alton, whose passionate advocacy of the anti-abortion case has led to an uneasy relationship with the rest of his party, it was the final blow.
'It is a Rubicon which I cannot cross. For me it is a life and death issue. Obviously in the circumstances I will not be able to stand again as a Liberal Democrat,' the MP said. He has held his Liverpool Mossley Hill seat since 1979 and said he would continue to serve in this Parliament.
Mr Alton's parliamentary colleagues expressed polite regrets at his decision but little remorse. Mr Ashdown said: 'It is sad that he feels he cannot stand again, but he has played no part in either the building of the party or campaigning for it for four years now.
'His departure, though sad, will not in any way alter the effectiveness of our party or our capacity to put our message across.'
Supporting the motion, Sara Tustin, chair of the Young Liberal Democrats of England, said: 'This is not a matter for political evangelism.' But for Mr Alton, a devout Catholic, abortion has been just that. In 1987 he resigned as the party's chief whip in order to bring in a Bill to lower the time limit for abortions from 24 weeks to 18. The measure was 'talked out', and since then Mr Alton has refused to take a portfolio.
The motion's supporters said the abortion law was interpreted leniently in some areas and strictly in others. Hilary Campbell, chair of the Women's Liberal Democrats, asked: 'Are we a party that says that legal medical procedures depend on the ability to pay?'
Approved by a large majority, the motion acknowledged abortion was an issue of individual conscience, but said the law should be applied consistently across the country. It said NHS employees must have the right to refuse to participate in abortions but must refer the patient to a colleague who is willing to do so.
Fuelling the controversy, an amendment was carried stating that NHS provision should ensure access to a legal termination within 14 days of one being sought. Lorna Spenceley of Harlow said this amounted to 'abortion on demand within a fortnight'.
Mr Alton's decision was supported by John Hemmingway, president of the Mossley Hill Liberal Democrats, and Lil Boughton, their acting chair. Mrs Boughton told the conference: 'I have always passionately believed that all life is precious and that it is simply not possible to achieve justice for women by injustices against their unborn children.'
Mr Alton, who did not speak in the hour-long debate, told a fringe meeting last night that the vote had not only created policy where previously none existed but would force doctors and nurses to refer patients for an abortion even if they were morally and ethically opposed to abortions.
Referring to a document on animal rights before the conference, he said: 'Rights will even be extended to goldfish in plastic bags on sale at fairgrounds. Isn't it a twisted irony that the same rights and concern for conscience is not extended to our own species?'
Sir David Steel, sponsor of the 1967 Abortion Act, regretted the conference vote and Mr Alton's decision. 'We have always got along on the basis of respected differing views. It is a pity that the party as a whole could not have let the matter rest there.'