There is no secure information about the historical origin of the FGM, but apparently it started long time before the rising of Christianity and Islam. Originally, FGM is not related to any religion.
It seems that early Roman and Arabic civilizations knew the practice which was linked to an ideal of virginity and chastity. These values are as we know very much cherished in the African and Arabic culture.
In ancient Rome it was done to female slaves to oppress sexual activity and raise their value. Herodotus talks about an Egyptian women being cut, around 500 a. C.
A widespread opinion is that FGM has its origin in the Egyptian culture. One of the theories says that in the Pharaohs’ beliefs the gods were bi sexual - so, in every human being there must be a male and a female part. The female part of the boy was located in his prepuce and the male part of the woman in her clitoris, and in order to become a full part of the male or female society, both needed to be circumcised.
Another theory says that it was performed by the Pharaohs to preserve their wives chastity during wartimes. A common name for the infibulation (see “classification”, p. 7) is “pharaonic circumcision” and may be related to this theory. The Somali name for this practice is “Gudniin Fircooni”, which means “remove according to the Egypt Pharaoh”.
Modern Egyptology though does not fully approve that FGM was practiced by the Pharaohs. Some sources tell about female mummies with traces of genital cutting. Other specialists deny this theory. The fact that many of the ancient Egypt medical doctors were Nubians leads to the idea that they brought the practice of FGM with them.
We know for sure that Female Genital Mutilation was never limited to the African continent. The Aborigines on the Australian continent performed Female Genital Mutilation and still do, at least in a few regions. Phoenicians seemed to have done it, the Hittites, the Ethiopians, the Incas in Mexico and ethnic groups in Amazonia and in the Philippines.
By the way, there is no trace of such a practice in the history of the North American native people.
During the 19th century in Europe, girls and women were cut to prevent masturbation and, related to it, mental diseases. Female homosexuality, nymphomania and hysteria were "cured" in this way. J. Marion Sima, “father” of gynaecology himself advocated this practice and found his followers.
In the Victorian England clitoridectomy with and without excision of the labia minora is related to Isaac Baker Brown, gynaecologist and surgeon who published in 1866 the results of his study on the curability of mental diseases in females. He was convinced that the clitoridectomy was the best choice for the treatment of sexual related disorders.
During this period, the female sexuality was denied, especially in the Anglophone upper and middle class. Sadly, such gross forms of surgery lacking any scientific base were quite widespread.
Apparently, the last known clitoridectomy undertaken for one of these reasons was conducted in 1953 in Kentucky.
The taboo about female sexuality and the related customs may be one of the reasons for the lack of historical information, as it is still presently the reason for the difficulty to get more precise data. The historical roots lead to a combination of beliefs, superstition, cultural and social values than to religious reasons. FGM remains a mystery. It seems as if in 2011 we have to close the historical chapter with the same word as it was used in 1992, referring to a source from 1981:
"In fact the origins have proved impossible to trace”.
 Brown, I.B., On the curability of certain forms of Insanity, Epilepsy, Catalepsy, and Hysteria in females, London, 1866
 Black, J., 1994, pp. 402-405
 Wright J. Female genital mutilation: an overview. J Adv Nurs 1996;24:251-9, cit. in: Conroy, R.M., 2006, p. 106
 McSwiney M.M., Saunders P.R., 1992, p. 136
Definition of FGM
How does it happen?
Who is concerned?
The Role of Men