Female genital mutilation increases the risk of complications during childbirth and infant mortality, the World Health Organization (WHO) has warned.
Women who have had the procedure are more likely to need Caesareans and the death rate among their babies is up to 50% higher, it said in a report.
The study, reported in the Lancet, involved 30,000 African women.
The practice is common in parts of Africa, where some believe it will maintain a girl's honour.
The report is the first of its kind to look into the long-term health consequences of female genital mutilation (FGM).
The WHO described FGM as a form of "torture" that must be stamped out, even if performed by trained medical personnel.
"By medicalising it, we will be endorsing this practice, this violation of a child's body and a basic human right of an individual and I think that's the worst thing we can possibly do," Joy Phumaphi, WHO assistant director-general for family and community health, told the BBC.
Women were studied in six countries in Africa - Burkina Faso, Ghana, Kenya, Nigeria, Senegal and Sudan.
However, Egyptian doctor Professor Munir Falsi denies that type 1 or type 2 FGM, which he calls "female circumcision" is cruel, or dangerous.
"With type 1 and type 2, there is no problem whatsoever with pregnancy or childbirth," he told the BBC's World Today programme, pointing out that 90% of Egyptian women are circumcised.
"Most of the complications are with type 3, which is understandable," he said.
The report accepted that the more extensive the mutilation, the more serious the risks but said all forms were dangerous.
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According to the report, mutilated women were 31% more likely to have a caesarean delivery, had a 66% higher chance of having a baby that required resuscitation and 55% more likely to have a child who died before or after birth.
"As a result of this study we have, for the first time, evidence that deliveries among women who have been subject to FGM are significantly more likely to be complicated and dangerous," Ms Phumaphi said.
The organisation says the new research is vital to protect communities in the future.
While many African countries have passed laws against FGM, the WHO says they are not being properly enforced.
FGM is practised in 28 countries, mostly in sub-Saharan Africa.
One hundred million women worldwide have undergone the procedure, which happens to three million girls under 10 every year. It is carried out by both Christian and Muslim communities.
The operation involves the partial or total removal of the external genital organs.