The Mexico City assembly has voted to legalise abortion, placing the capital of the second-biggest Catholic country on a collision course with the Catholic Church.

Defying warnings that they would be excommunicated, deputies voted 46-19 in favour of allowing the termination of pregnancies in the first 12 weeks. Penalties for women who have abortions after that time will also be cut, from as much as three years in prison to community service in most cases.

Nationally, Mexico allows abortions only in cases of rape, if the woman’s life is at risk or if there are signs of severe malformations of the foetus.

Pope Benedict XVI had intervened personally in the debate, sending a letter to Mexican bishops ordering them to oppose the measure. Conservatives also mounted an emotional campaign against the Bill, publishing symbolic death notices in newspapers and carrying tiny white coffins through the streets.

Campaigners for the Bill were jubilant today, saying that the vote would save the lives of thousands of women. An estimated 200,000 women have illegal abortions in the country every year, and about 1,500 die as a result.

“This is an affirmation of the rights of women in Mexico City,” said Esthela Damián, a deputy from the left-of-centre Party of the Democratic Revolution (PRD). “I am very happy about something that we women deserved.”

Opponents of the measure reacted with anger, vowing to challenge the decision in the courts. “They did not listen to the citizens,” said Mariana Gómez del Campo, president of the National Action Party (PAN) in Mexico City. The conservative Catholic PAN is the party in power nationally.

Polls indicate that a majority of the 8.5 million residents of Mexico City were in favour of the measure. However, the country as a whole is evenly divided on the issue. Riot police had to keep protesters from the two camps apart after they hurled insults at each other before the vote.

Felipe Calderón, the President of Mexico, who is a PAN member, has largely stayed out of the debate. But his wife, Margarita Zavala, expressed her opposition to the Bill.

The Mexico City assembly has clashed with the Catholic Church before. It recently allowed same-sex civil unions and is debating whether to legalise euthanasia.

The Archbishop of Acapulco, Felipe Aguirre Franco, said that MPs who had voted to legalise abortion would “get the penalty of excommunication. That is not revenge, it is just what happens in the case of serious sins”. It is the latest loss suffered by the Vatican in its former bastions of Latin America and southern Europe. Portugal recently voted in a referendum to legalise abortion, and same-sex marriage was approved in Spain nearly two years ago. The Pope is due to visit Brazil next month in an effort to shore up the Church’s position in the most populous Catholic nation.

He will try to halt the loss of worshippers to Protestant evangelical groups and check the influence of left-wing “revolution theology” priests on the poor.

Mexico has the second-largest number of Catholics after Brazil — 90 per cent of its 106 million people — but the grip of the Church there has also weakened in recent years.

The decision of Mexico City to legalise abortion highlights the growing cultural divide on display in last year’s fiercely contested presidential election.Only a few hundred thousand votes separated Mr Calderón from the PRD candidate, Andrés Manuel López Obrador. Mr Calderón’s votes came mainly from the Catholic and relatively prosperous north, while Mexico City and the south voted strongly for the losing candidate, a former Mayor of Mexico City.

Left-wing politicians were triumphant today, saying that the vote had shown that Mexico was more socially liberal than people had imagined.

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