The controversy began when news emerged from Pernambuco, a poor state in the north-east of Brazil, that a nine-year-old girl who had been raped was pregnant with twins.
It is alleged that she had been sexually abused for years by her stepfather, who is also suspected of sexually assaulting an older disabled sister. He is now in prison.
Public interest in the case soared when the local Catholic archbishop tried to block the girl from having an abortion.
Brazilian law allows abortion only if there is a risk to the life of the mother or in cases of rape. Doctors said the girl met both those conditions, and said she was so small her uterus was not big enough to carry one baby, never mind two.
Opponents of abortion say the girl could have safely had a Caesarean section.
In the end the abortion went ahead and the local archbishop, Jose Cardoso Sobrinho, said all those adults involved - the mother and the medical team - had been excommunicated.
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The archbishop later insisted it was not he who was ordering the excommunication, but that he had been simply restating the teachings of the Church.
His statement attracted widespread condemnation, led by Brazil's President Luiz Inacio Lula da Silva, who said as a "Christian and a Catholic" he deeply regretted the bishop's conservative attitude.
Archbishop Sobrinho then added to the storm of protest by saying that while the stepfather had allegedly carried out a "heinous act", excommunication did not automatically apply to him.
The controversy then spread to Rome where it appears to have provoked a surprising divergence of opinion at the highest levels.
Unforeseen consequences
One senior Vatican official appeared to back the Brazilian archbishop and then another to sharply contradict him.
It seems, however, the controversy may have led to other consequences in Brazil that Archbishop Sobrinho did not foresee, and which almost certainly he would not have welcomed.
Those who would like see a more liberal law on abortion say the fact that the Brazilian state - from the president down - rallied so firmly to the side of the doctors involved in this case will give renewed courage to their medical colleagues across the country.
Even in circumstances where abortion is legal, it seems doctors here have proceeded nervously, fearful some say of a negative reaction from the media or the Roman Catholic Church.
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Anibal Faundes, professor of obstetrics at the University of Campinas, says legal abortions - of which there were 3,053 between January and November in 2008 - are now carried out in around 500 hospitals in Brazil, mainly in Sao Paulo and the south-east of the country.
He is clear about the most important consequences of the case involving the girl in Pernambuco.
"Everybody realised that Brazil is in favour of abortion in case of rape and risk to the woman's life," he says emphatically.
"That was not clear before. But during the last two weeks it was perfectly clear if you are against abortion after rape and abortion when there is risk to the life of the person then everybody will be against you.
"That is what changed in the last two weeks."
"Those within the Church that are extremely conservative with respect to this subject have lost a lot of ground," he argues.
'Life must be protected'
Cardinal Odilo Scherer, archbishop of Sao Paulo, was reluctant to be drawn on the specific issues of the recent controversy.
Speaking generally, he told the BBC News website that the position of the Church in relation to abortion in cases of rape or a threat to the life of the mother was the same everywhere in the world.
"The Church's position is always to defend life and trying all that is possible to first avoid these things happening, for this we need proper sex education, to teach people how to behave, in a socially responsible way.
"Secondly, to do everything possible to ensure life is protected, because no matter what happened to create this life, even if it was through violence, it will always be considered a human being, a helpless and defenceless human being.
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"I can understand how a woman who is carrying a baby after being violently raped feels, but there is always a possibility to help this woman to cope with this situation. There are many ways today that the medical profession can help to save the lives of this woman and child."
He concedes, however, that some damage may have been done to the Church's position.
"It is possible, yes, that it has," he says. "All this publicity, this criticism that was made of the Church has in some form weakened the position of the Church in defence of life and against abortion."
Bleak
The case has also renewed attention on illegal abortions in Brazil - at one million per year, estimated to far outnumber legal procedures.
Every year, about 200,000 women seek medical help from the state system after having sought illegal procedures in back-street clinics.
Outside a bleak and graffiti-covered building which was once an abortion clinic in Sao Paulo, but which has now been closed by the authorities, Andrea has grim memories.
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"I [went through] the process and I wasn't left with any ill-effects," she says of the illegal procedure.
"But this place was pretty much a like a butcher's shop. There was not any preparation, psychologically or clinically."
When the clinic was closed, police said they found a secret corridor leading to a room where the patients stayed. Out-of-date medicines and syringes believed to have been reused were also discovered.
For those with more money, there is access to better facilities.
Paula paid 2,000 reais ($890; £610) for her abortion but says she was not concerned about the clinic, as it appeared to have acceptable standards. She says she had an abortion because she was in the middle of a separation, and couldn't afford to raise a child.
"It was clean and bright. It was a big fancy place, and a lot of girls were there with mothers and boyfriends."
Abortion - both legal and illegal - seems certain to be an issue that will make headlines again in Brazil in the not too distant future.
The Catholic Church may have been temporarily pushed onto the defensive, but it regards the issue as a crucial moral battleground, and is certain to return to make its case with renewed vigour in the months and years ahead.
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(Source: BBC)