In an effort to improve boys performance in reading and writing, and girls performance in math, teachers at the school found research that shows separating boys and girls and tailoring lesson plans just makes sense.
"Brain research says boys brains develop in a different pattern, not a better pattern but a different pattern than a girls brain," Director of Instruction and Student Achievement Robin Gilbert said.
Standardized testing confirms it has made a big difference. Since they started the program, 10 point differences are no more.
"The gap is still close between achievement in boys and girls," Gilbert said.
But excitement for this coming school year is replaced with uncertainty.
"We believe that perpetuating gender stereotypes with single sex classrooms limits opportunities for boys and girls alike," ACLU representative Allie Bohn said..
The ACLU filed a complaint with the Office of Civil Right in the Department of Education. Federal investigators came to the school this spring.
"We were left with good feelings on it, we answered all their questions. We submitted all the paperwork and now they've done interviews with all the teachers. Now we just wait," Gilbert said.
The ACLU actually filed a complaint against a school district in Birmingham, Alabama around the same time as Middleton. After dealing with the Federal Department of Education, school leaders there already dropped single sex classrooms.
"So they entered into an agreement with the office for civil rights and basically came to the conclusion that there was no way they could bring their single sex program into compliance. With the federal law and so that's why they abandoned it. ACLU believes Middleton will end the same way."
Middleton is waiting for the ruling and there are three possible outcomes. The Office of Civil Rights could say the program is in compliance. It could require some changes to become compliant. Or it could rule Middleton's same sex classrooms are illegal.
"We have followed the law the whole way. What we're doing is legal and our data shows that it's effective. So I would be shocked if there were any way that they would say that we're totally out of compliance."
"Under the Constitution the government needs an exceedingly persuasive justification for separating kids by sex. That's a strict test that most programs are unable to meet," Bohm said.