Cooties is a term children use refering to something that is bad, dirty, gross etc. For example children will often refer to another person as having cooties like saying "don't touch him (or her) they have cooties" , it is not a real word, it is just slang.
Thankfully, males do not carry cooties. Only females carry them. Highly contageous- and you can pretty well assume that if you get them, then your elementary school life is over!