There appear to be several write-ups here about female genital mutilation and male genital mutilation, but surprisingly, I couldn't find any about intersexed genital mutilation. This struck me as a bit odd, as ratio wise, a far greater proportion of intersexed individuals have nonconsensually had their genitals mutilated, at least in the USA and the UK.
The theory goes something like this: a baby is born, and this baby has ambiguous genitalia. An enlarged clitoris, fused labia, a tiny penis, something along those lines. In short, the genitals are not entirely female or entirely male.
What happens is the doctor gets rather worried and calls for an "emergency" operation to have these genitals "fixed", even if they function perfectly well.
According to modern society, people can only be male or female; anything else doesn't exist and can't legally be put down on a birth certificate, driving license or passport. Then again, in America, tomatoes are legally a vegetable.
Lest these babies grow up illegally and have to point out to people throughout their whole lives that they do exist, they're not male or female, and they're quite comfortable with that, immediate action is taken. The doctor chooses a binary sex for the baby. This is usually whichever most closely resembles their genitalia's current state. Then they perform surgery on the baby to make the genitalia match the sex chosen for them. Needless to say, the baby is too young to consent to such an operation. Not that it matters much, as parents are usually encouraged to keep the baby's real sex a secret, even from the baby. Many intersexed people at least reach puberty before they realise something is wrong, and only then manage to get the truth from their parents.
The main problem with this is that most people have an inherent sense of what their gender is. Just because your genitals were changed to resemble that of a girl's doesn't mean that you will feel like, or indeed be, a girl (or vice versa for people whose genitals were changed to resemble that of a boy's). Once you're old enough to work out what your gender is you can always have your genitals surgically altered if they don't match it. The main problem here is that many intersexed people's genitals have already been altered in the other direction, which makes any further surgery very difficult. Some intersexed people identify as intergendered, meaning their gender itself is not completely male or female. If this is the case, then the best solution would have been to never have surgery at all, but they were too young to object at the time.
That's just the surgery side; there's also trouble caused by your parents making you take testosterone or oestrogen, but that's another matter and one that's slightly harder for them to lie to you about.
In conclusion, although it's possible to mutilate someone's genitals, it doesn't mean that person will grow up to think that it was the right thing to do, even if you give them pills and try to deny that anything happened. Most intersexed people agree that it's best to just leave their bodies alone and let them make their own decision about how to alter it, when they're old enough.
For more information on how mutilating someone's genitals and giving that person hormones and lying to em about eir past does not affect eir gender, see David Reimer's life.
As someone pointed out to me after writing this, there are many other bad points of lying to a child about eir sex and trying to change it without eir consent. Knowing there's something "wrong" with you that no one will talk about can't be very easy to go through. I'd recommend browsing http://www.isna.org/ as there's much more to this.