James DeMeo examined this question. In his analysis, most of the world's genital cutting traditions could have a single origin in northeast Africa or the Middle East prior to the Dynastic period in Egypt (c. 4000-3500 BC).

The underlying psychology of both male and female genital mutilations is anxiety regarding sexual pleasure, mainly heterosexual genital intercourse, as indicated by the associated virginity taboos and ritual absolutions against vaginal blood. In the final analysis, these mutilations say more about predominant sexual attitudes than anything else.

Given their similar distributions, similar cross-cultural aspects, and similar psychological motifs, the time and location of origins of male and female genital mutilations are probably identical, the use of each being mandated and widely expanded by groups where dominance of the sexual lives of children by adults, and of females by males, was most extreme. The use of eunuchs has died out over the last 100 years with the decline of the harem system, but female infibulation and other forms of female genital mutilation persist in accordance with the arranged marriage system, and other vestiges of a powerful and hysterical virginity taboo.

Based upon the geographical distributions of the mutilations, it seems reasonable to assume that they began somewhere in the eastern part of North Africa, or possibly even in Arabia, prior to the Dynastic period in Egypt (c.4000-3500 BC) in association with a major climatic change which affected North Africa and the Near East at this same period. Thereafter, the mutilations were spread by the inhabitants of these regions, in accordance with their customs and beliefs, following historically-recorded migratory pathways. Nearly every male-dominated patriarchy which developed within North Africa and the Near East, up to and including more recent Moslem Empires and later Moslem nation states, adopted and further spread the mutilations. Over the centuries, ocean-navigating peoples from these same regions spread the practices out from the Red Sea and Persian Gulf regions to places as far removed as Indonesia, New Guinea, Borneo, and other areas now inhabited by Moslem peoples. Genital mutilations in Australia, central and eastern Oceania and the Americas may have arisen independently; but even here, as discussed above, Pre-Moslem and Pre-Columbian diffusion of the traits is strongly suggested by the mapped geographical characteristics, and cannot be ruled out.

James DeMeo. The Geography of Male and Female Genital Mutilations in Sexual Mutilations: A Human Tragedy. George Denniston and Marilyn Milos, Editors, Plenum Press, NY, 1997, p.1-15.