Boys are forging ahead of girls in three prestigious university admissions tests following years of female achievement at GCSE and A- level.
Males outperformed females in a pound;1.6 million trial of a US-style university aptitude or "SAT" test - not to be confused with the English Sats regime - taken by 9,000 pupils.
Boys are also outstripping girls in the BMAT test used by five leading universities, including Oxford and Cambridge, to select medical school applicants.
Additionally, it has emerged that Oxford University's history exam has been dominated by boys, despite girls doing better at A-level.
These findings, presented to a conference run by the Nuffield Review of 14-19 education, raise questions about girls' recent dominance of higher education entry.
Universities are increasingly setting their own admissions tests to supplement the information they receive from school exams. If boys continue to perform better in these, it could have a long-term effect on admissions.
Females are ahead of boys in almost all GCSE and A-level subjects. Last year, 59 per cent of UK undergraduates were women.
The findings will feed into the debate about whether GCSEs and A-levels favour girls. The SAT test and the BMAT are one-off mainly multiple-choice tests, while school exams reward hard work over the length of a course and have more essay questions, which girls are widely said to be better at.
Professor Alison Wolf, of King's College London, said: "People have been saying for years that there are genuine issues with gender bias in school assessment. It's now time we took this seriously. We have a set of exams that are concentrating to an unreasonable degree on sets of skills that girls are better at. It's clear from these results that there are other sets of skills that boys are better at."
But Professor Jo Boaler, of Sussex University, said: "The last thing we need in education is US-style SATs, which for many years have stopped women from entering American colleges because they under-predict the performance of females. Girls' improved school performance is not down to testing bias."
The SAT trial has been backed by the influential Sutton Trust charity as a potentially fairer university selection device than A-levels alone.
The five-year pilot will finish in 2010, but the Government is not committed to introducing the test. Researchers plan to investigate whether it is biased towards boys.
Professor Peter Tymms, director of Durham University's Centre for Evaluation and Monitoring, said: "The nature of a test may favour one sex or the other. Over time, GCSEs and A-levels have become slightly more girl-friendly."
Exams could be changed to allow a wider range of attributes, such as creativity and lateral thinking, to be measured - possibly with a "pupil profile", reported alongside grades.
Tim Oates, of Cambridge Assessment, said the BMAT findings were in line with the fact that more boys than girls were choosing to take single science GCSEs, which provide a better foundation for the knowledge required in BMAT questions.