But Kim Gandy, president of the National Organization for Women, said separate classrooms reinforce gender stereotypes. “A boy who has never been beaten by a girl on an algebra test could have some major problems having a female supervisor,” she said. While some advocates believe that girls are more likely to participate in class when no boys are present — and that boys, particularly those from low-income families, tend to focus better without girls around — academic research is inconclusive.

“The question always must be: What are you trying to accomplish with separating the students and how will you do it?” said Rosemary C. Salamone, a law professor at St. John’s University and author of “Same, Different, Equal: Rethinking Single-Sex Schooling.”

She added, “If you don’t do it thoughtfully, you run the risk of reinforcing stereotypes and playing to students’ weaknesses.”

In California, a high-profile governor’s initiative that split six middle schools and high schools into single-sex academies in the late 1990s ended after a few years, and few students showed sizable improvement.

At the Bronx’s Eagle School, there is also little evidence so far of improvement, at least of the easy-to-measure variety. Students of both sexes in the co-ed fifth grade did better on last year’s state tests in math and English than their counterparts in the single-sex rooms, and this year’s co-ed class had the highest percentage of students passing the state social studies exam.

But these numbers are as much a reflection of who is in which room. In general, struggling students are steered toward the single-sex classes (anyone who objects can opt out). While test scores might not show it, Mr. Cannon and his teachers said there have been fewer fights and discipline issues, and more participation in class and after-school activities, since the girls and boys were split up.

Mr. Napolitano, one of four men among the school’s 30 classroom teachers, said he thinks of his students as “23 sort-of sons,” and engages them with Marvel Comics and chess. He proudly held up the book “Patrol Boy,” with a picture of a young man with a large tattoo on his back, as an example of material he would not have used in a co-ed class.