Cooties (occasionally spelled coodies) is an imaginary disease that little boys say little girls have.
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To the best of my knowledge, there is no such thing as an equivalent to "cooties" in French "childhood culture", either in Europe or North America. You might find references to the other sex being icky, but I have never seen it "formalized" as something like it is in English.
I'm French. The best translation I can think of is (apparently as "cooties" is an insult boys against girls) "les filles c'est nul" or "les filles ça craint" (not "ça craint / It's scares" but "ça craint / it's the shame of being with, it's boring". Literary translation would be "les filles c'est des pouilleuses", "the girls are dirty / verminous person", but it is not something the child say in real life. This is too "nasty" and the parents scold probably, while "les filles c'est nul" they can smile.