The division is based on a controversial book that claims that girls and boys brains respond differently in school.
"What happens is these boys, in particular, tune out. They're not paying attention. They need schools that understand what is best for a six-year-old girl is not what is best for a six-year-old boy," said Leonard Sax, the author of "Why Gender Matters."
The ACLU is suing the education department to stop the separate gender classes. It says, "We've spent years in this country fighting the idea that boys and girls should be treated differently."