The term is thought to have originated in the trenches of World War I, but its origin is uncertain, especially in light of the fact that the term is unknown in the UK and Europe. It may derive from the Malay word kutu, meaning biting insect.
A well-known toy is the Cootie Catcher, a folded paper arrangement that can reveal one or other internal surfaces when manipulated by hand. One surface is blank, the other drawn with dots representing the cooties. The joke is to show the blank side, then run the toy through a person's hair, revealing the dotted surface. The toy is so designed that the appearance of either surface is outwardly the same apart from the "cooties". A variation of the same toy is known to British schoolchildren (and in some locations in the US) as the Fortune teller.
Cooties have been referred to in a number of episodes of The Simpsons, possibly baffling non-American viewers.