Statistically speaking, that's not so. About .0001 of the school age cohort.
School districts with 10,000 or more students might have one, and then you have the issue of level of presentation. Some are barely noticeable, some are middle, and some are pronounced. If I had a child with fairly obvious male genetalia, I'd have them checked out. So let's say we're now at .00005.
I remember when I was about 5 or 6, the woman who babysat us while my mother worked had a baby. I kept calling it a girl, and the mother kept correcting me that it was a boy. I have often wondered whether that child had a milder form of that disorder (now that I’m old enough to know about genetic disorders).
A poster above suggested that school policies should strictly be based on the presence of XX or XY chromosomes; my point is that even a genetic test is not absolute proof. A school district cannot have an absolute policy that XY will be treated as boys and XX as girls, when there is a small number of XY who are born as physiological girls. These individuals are not in the same category as “transgenders” who are clearly pretending to be someone of the opposite gender.