Diseases that the opposite sex has that gives you a reason to not be around them. When you get older, cooties becomes known as "STDs."

A pubic hair piece. A toupee for the pubic area/genitals. In the 1700’s when mercury was used to treat sexually transmitted diseases (Gonorrhea or Syphilis) one of the side effects was the loss of pubic hair. To disguise this condition, that was not cured by mercury, a Merkin was employed.

US slang that references childhood:

Cooties are an imaginary affliction from childhood.

When children reach the age where they notice the sexes are different the children claim a member of the opposite opposite sex will give you "cooties" if they touch you.

Its a way of little girls telling other little girls not to play with boys and vice versa

An age-old disease only found in young children. all children have this disease, but the boys have a different type than the girls. because of this, touching or being touhed by a member of the opposite sex is fatal, since you have gotten their cooties.

The metaphysical manifestation of the fear of social backlash resulting from association with the opposite sex during childhood.

In short, the other sex has them, you can get them, and you do not want them.

Highly Contagious, Viral batecteria that breed inside young females and are released into the air via sweat glands when in the proximity of other young boys.
Various forms of protection include, Sprays, Suits, and name calling.

Imaginary infestations of the truly un-cool.