“We know we’ve got a crisis, and the crisis is with boys,” said Elaine Kamarck, a resident scholar at Third Way and a former Clinton administration official. “We’re not quite sure why it’s happening.”

Two of the leading theories involve single-parent families and schools. The number of single-parent families has surged over the last generation, and the effect seems to be larger on boys in those families than girls. Girls who grow up with only one parent — typically a mother — fare almost as well on average as girls with two parents. Boys don’t.

But the trends seem too broad for family structure to be the only cause. That’s where schools come in.

Girls enter school with a lead on boys, and schools then fail to close the gaps. Instead, they increase. The behavioral advantage that girls have over boys in kindergarten, based on teachers’ assessments of their students, are even larger in fifth grade.

By then, the average girl is at the 60th percentile of an index of social and behavioral skills, while the average boy is at only the 40th percentile, according to Claudia Buchmann of Ohio State and Thomas DiPrete of Columbia, the authors of the new paper. That gap of 20 percentage points is larger than the 14-point gap between poor and not poor children or the 15-point gap between white and black children.

These behavior measures are subjective, of course, based on the views of teachers across the country in very different classrooms. Yet it’s clear that the measures reflect something real, because the behavior differences later translate into academic differences. By high school, even advanced math and science classes now have more girls than boys. At college graduation ceremonies around the country this spring, women in caps and gowns will easily outnumber men.

The experts who study the subject disagree on the solutions. Some, like Ms. Buchmann and Mr. DiPrete, point out that boys still do quite well in the best-performing schools. When good grades bring high status, boys respond. To the researchers in this camp, the answer involves improving schools, which will have a disproportionate effect on boys, rather than changing schools to be more attuned to boys’ needs.