An analysis of the first advanced extension awards, aimed at the cleverest 1 per cent of upper sixth-formers, shows that boys outperformed girls in 14 out of 16 subjects.
Results from the 7,000 entries show that boys perform better at the very highest level, even in traditionally "feminine" subjects such as English. Girls outclassed boys only in critical thinking and French.
A total of 17.3 per cent of boys gained distinctions in the extension awards, compared with 16 per cent of girls. More than a third of males got the top award in English - 11 percentage points more than girls. In German the gap was 8 points and in maths 15 per cent of boys got a distinction compared with 10 per cent of girls.
One in three sixth-formers who sat the tests was from a private school. Around 1,000 more entries were from boys than girls. English, maths and physics were the most popular subjects.
Results suggest that, if the Government introduced a distinction A-level to distinguish between A-grade candidates, boys would win more places at leading universities.
However, GCSE results out this week show the gender gap has widened marginally in girls' favour.
While the proportion of teenagers of both sexes getting C or better rose, the figure for girls is 62.4 per cent, compared with 53.4 per cent for boys.
Girls outperformed male students in virtually all subjects at all grades in both AS and A-level.
The spread of boys' exam results shows they are more likely to feature at the extreme ends of the distribution - performing either very well or very badly. Girls tend to bunch round the mean grades.
Professor Alan Smithers of Liverpool University said: "Although the results of young women are continually improving, it is still men who succeed at the top level. This could explain the significant number of prominent males in many walks of life and why we still have the glass ceiling."
Men get a higher proportion of first-class degrees than women, though the gap has been narrowing.
The future of the extension award is in jeopardy, despite backing from the Qualifications and Curriculum Authority, which developed it.
Other options to rank straight A students include a new A* grade awarded to the top 5 per cent, and reporting marks alongside grades.
Elspeth Insch, head of King Edward VI girls' school, Handsworth, Birmingham, said: "I do not think that boys are genetically cleverer than girls, but clever boys can be superbly confident.
"These tests were held at the end of the exam season. Boys are more willing to take the risks that count in these exams."
Bethan Marsall, English lecturer at King's College London, said: "It is interesting that these figures have not been headline news.
"It shows how sexist we still are that when girls do better, civilisation is at an end, but when boys do better it is taken as confirmation that they are secretly cleverer."
GCSE results, 6-7