A new, city-funded school, Excellence Charter School, will open its doors in September to kindergarten and first-grade pupils in Bedford-Stuyvesant. The school will be open to boys only. In nearby Williamsburg, however, about 80 students are struggling to keep their pre-kindergarten program after the city cut off funding because, in this school, boys and girls learn separately.

The city agreed to give $256,000 to Williamsburg’s Yeshiva Yesode Hatorah in 2001 to begin pre-kindergarten classes. The school hired teachers and enrolled pupils. The demand was so great that the yeshiva, which serves Orthodox Jews, expanded its preschool into a new building and financed the renovation.

But then the city education department announced it wouldn’t come through with the money. The reason it gave was that boys and girls were to attend separate classes. Unwilling to turn needy families away, the yeshiva went ahead with the program without the city’s support. The school says it now faces financial trouble.

New York’s Education Department does support other forms of single-sex education in addition to Excellence Charter School. New Explorations into Science, Technology and Math, a school on the Lower East Side, began offering single-sex math and science classes for grades six through 12 in the 2002-03 school year. East Harlem’s Young Women’s Leadership Academy has been providing public single-sex education — despite the objections of the National Organization for Women and the American Civil Liberties Union — since 1996.

The all-girls school has been so effective at helping poor and minority pupils attend college that Senator Clinton once praised it on the Senate floor, noting that “single-sex schools and classes can help young people, boys and girls, improve their achievement.” For this reason, she added,”there should not be any obstacle to providing single-sex choice within the public school system.”

We agree with Mrs. Clinton. The Education Department has said that it will only permit single-sex education if there is an identifiable pedagogical reason for it. While studies have shown that middle and high school pupils perform better in a single-sex environment, there is no research to show that pre-K youngsters would do so as well. None of the experts we talked to said there was research showing benefits to single-sex education for kindergarteners, either.

Which leaves it an open question why a single-sex kindergarten is okay at Excellence Charter School in Bedford-Stuyvesant, but single-sex pre-kindergarten at Yeshiva Yesode Hatorah in Williamsburg is, for the city Education Department, not kosher.

“It’s crummy to deprive these 4-year-olds because you don’t agree with the religious convictions of their parents,” says City Council Member David Yassky, whose Brooklyn district contains the yeshiva.

The city’s Education Department also says that a federal law, Title IX of the Education Amendments of 1972, prohibits it from funding a single-sex preschool. But Title IX was never intended to prohibit single-sex education — the issue isn’t even addressed in the statute.

As is often the case, however, federal bureaucrats have written regulations expanding the law beyond its literal requirements. The regulations implementing Title IX permit single-sex schools, provided each gender receives comparable courses, services, and facilities. But they did prohibit same-sex classes within a given school, with the exception of sex-education and gym classes.

Thanks to Mrs. Clinton’s leadership, an amendment to the No Child Left Behind Act has removed the regulatory obstacles to single-sex education in the public schools. So, in the fall, New York will see four new publicly funded single-sex schools open their doors — alongside the 217 single-sex private schools currently operating in the five boroughs.

The No Child Left Behind Act only addressed elementary and secondary schools, overlooking Williamsburg’s preschoolers. They are now at the mercy of federal regulations that — stay with us here — deem single-sex classes acceptable for kindergarteners but not for pre-kindergarteners.

An Albany school that includes kindergarteners got around these rules before it was changed by organizing itself as two schools, Brighter Choice Charter School for Boys and Brighter Choice Charter School for Girls. They have the same principal and the same school building. Rather than closing the place, the federal Education Department gave it a $4 million grant and said it had the potential to be a national model.

In March, Mayor Bloomberg announced that his administration would commit more than $500 million toward “making pre-kindergarten education truly universal in our city” because, he said, “research on early childhood learning and school achievement shows that investment at ages 3, 4, and 5 pays off.” If the city is to achieve this goal, it is going to need to show some flexibility and creativity in working with all of the city’s diverse communities — the ones in Williamsburg just as much as those in East Harlem and Bedford-Stuyvesant.