The 193-page report from the Equal Opportunities Commission found that boys failed to improve their GCSE performance as much as girls over the period and their results lagged well behind in English, humanities, arts, modern languages and technology.
Even in the traditional male strongholds of maths and physics, girls are now matching boys at both GCSE and A-level.
The report compiled by Cambridge and South Bank universities offers the most comprehensive evidence yet of the extent to which boys are falling behind girls. Recently, Chris Woodhead, the Chief Inspector of Schools, highlighted the underachievement of white working-class boys.
The researchers argue that cultural changes have led to higher expectations of girls while the disappearance of many traditional working-class jobs has demotivated some boys. At A-level, boys still do better in English, modern languages, history, technology and chemistry but the gap is narrowing. Girls do better in biology, social studies and art and design. Boys also get more vocational qualifications than girls.
Madeleine Arnot, one of the authors, said it was misleading to talk about boys' underachievement. "We have a success story here. This is an excellent sign of the work schools have done to improve girls' performance so that they are now catching up."
The researchers looked at girls' and boys' performance in relation to their proportion of entry to exams. The comparisons are based on figures for those getting five or more A-C grades at GCSE and of A and B grades at A-level.
The year-long study of exam results between 1985 and 1994 examined the effect of recent education reforms on equal opportunities. It found that the improvement in girls' performance predated the start of the national curriculum and the 1988 Education Reform Act.
However, the national curriculum has helped to ensure that, at 16, girls are now taking "male" subjects, such as science, which they shunned in the past, Boys predominate only in chemistry and economics; girls only in social studies.
However, the report emphasises that girls still have some way to go. At A-level they still avoid traditionally male-dominated subjects such as physics: boys now account for an even higher proportion of entries in physics and technology than they did 10 years ago.
Girls do slightly better than boys at physics, probably because they are such a small group. The proportion of girls taking chemistry and maths also lags that for boys.
Yet more boys are now taking "female" subjects such as English and modern languages at A-level.
Young men under 21 also achieve more vocational qualifications and young women opt mainly for traditional female courses such as hairdressing and beauty and care.
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