The move is designed to gather more information on the practice, which was outlawed in the UK in 1985, and to help women at risk.
It comes ahead of the United Nations' Day of Zero Tolerance to FGM on Thursday.
At least 66,000 girls and women in the UK are believed to be victims.
The Department of Health says from April, all NHS hospitals will be able to record if a patient has undergone FGM or if there is a family history of this.
By September, all acute hospitals will have to report this data to the Department of Health, on a monthly basis.
Continue reading the main story Somalia - more than 97% of women aged 15-39 have been cut in this way Guinea - 99% of women aged 35-39 and 89% of those aged 15-19Egypt - 96% of women aged 35-39 and 81% of those aged 15-19Sierra Leone - 96% of those aged 35-39 and 75% of those aged 15-19Source: International Development Committee, June 2013The government says this is the first stage of a wider scheme to improve the way the NHS will "respond to, follow-up and support the prevention of FGM".It is hoped this will, in the autumn, provide the first snapshot of how many women have been treated by the NHS for FGM, and in the longer term, help identify families where girls might be at risk.
So far, no-one in the UK has been prosecuted for carrying out FGM.
Campaigners say there is a lack of knowledge about how common the practice is and where it is happening and that this is hampering social services and the police in the collection of evidence.
Comfort Momoh, who runs the African Women's Health Centre at Guy's Hospital in London, says FGM is "a big problem in the UK" and that health workers need to be better-informed about it.
"We have people migrating from different parts of the world coming to the UK, to the West, bringing their cultures, bringing their own traditions, so it is a big problem - and it is growing - so as a front-line provider we need to educate ourselves.
"We need to be aware of what to do and how to safeguard children and girls."
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