At 14, boys are holding their own in maths, and are on a par with girls in science, according to a TES Cymru analysis of 2005 key stage results. But their literacy skills are way behind the girls - and their peer group in England.
Meanwhile, Welsh girls widened the gap for five or more GCSE or equivalent passes at grades A*-C, from 10.6 to 12 percentage points last summer. The male pass rate was 46.3 per cent, compared to 58.3 for girls.
Figures from inspection agency Estyn show boys are more likely to underachieve, be excluded from school or break the law. But targets for reducing boys' underachievement, contained in the Learning Country, the Assembly government's 2001 education strategy, have been dropped from a new revised version.
A government spokeswoman said the chief inspector's last annual report confirmed that, at key stage 3, "many schools now have useful strategies to improve boys' language skills".
"We are aware that there is work to be done to close the gender gap across all key stages. But overall performance for boys and girls is improving all the time."
Heads said the government's 14-19 reforms, intended to widen the range of vocational and work-based courses, should help.
Chris Howard, head of Lewis Pengam boys school, Caerphilly, said: "The national curriculum has been too girl-focused. Geography used to be about rocks - now it's overwhelmingly focused on human geography.
"Putting on more hands-on vocational courses will benefit girls but have more impact on boys," he added.