James Dalziel, head of Eastbank Academy, Glasgow, raised the issue with Helen Liddell, Labour's education spokeswoman, and the theme was followed up in an address by Peter Downes, former president of the Secondary Heads Association south of the border and head of Hinchingbrooke School, Huntingdon.
Professor Lindsay Paterson of Moray House Institute said he had observed a widening gap between girls and boys which began in the late 1970s.
Mr Dalziel pinpointed boys' performance as a major weakness of comprehensive education. It had done "wonderfully well" for girls who were outstripping boys. In Standard grade courses at Eastbank, for every two credits girls achieved, boys got one. "It's getting worse year after year," Mr Dalziel said. The system had been so busy changing structures, it had missed this basic flaw.
Mr Downes, who has researched the issue and taken positive discrimination measures in his own secondary, said that girls had been out-performing boys for many years and it was a worldwide issue.
In England, there was a 10 per cent variation between girls and boys in exam performance, a position he believed was mirrored in Scotland. A few years ago, in a year group prize-giving at his school, of the 30 awards, 29 went to girls.
Mr Downes said it was not a secondary problem as he outlined strategies to combat disadvantaged boys. It was only manifested at the later stage and pinpointed the vital importance of reading success in nursery and primary. "We need to make parents of children under five aware of their absolute crucial influence when they talk to their children," he said.
In Finland, which he believed was the only western country not to share the problem, all children from three onwards went to nursery until starting at primaries at seven. From then on, the focus was on reading in classes no bigger than 20 for the first two years. Almost every child could read, with immediate reading recovery programmes initiated for those with difficulties.
Mr Downes said girls learned to read before boys. They were more sensitive to talk and played games involving talk. "Boys will play games which involve doing things or hitting things or watching things," he told the conference.
Children grew up in a female environment and often lacked male role models at home and in school, where nine out of 10 primary teachers were women. Boys quickly became alienated in infant schools .
"In secondaries, girls will talk to each other or talk about boys, often older boys. Boys are thumping each other, or playing football," he said. Boys got status in non-academic ways by being tough, swaggering about and being in the football team. They stopped reading and became fascinated by computers. Estimates suggested 20 per cent of boys were addicted to computers by the age of 14.
Mr Downes said that boys over estimated their ability and girls under estimated it. Boys expected to get results without work.
Tackling underachievement across schools and raising awareness among staff was the first step in combating the problem, he said. Schools had tried different strategies, including setting up single-sex teaching in mixed comprehensives. In an experiment in Essex, both boys and girls had done better when they were "gender set".
Girls said they liked not having boys clowning about so that they could concentrate. The boys' group was more competitive and teacher-focused. Boys liked reaction with teachers.
Other schools, Mr Downes continued, had targeted disaffected boys in the first year of secondary by praising them quietly, setting them competitions and taking them on visits. School ethos was important and making academic success acceptable to boys.
Other initiatives included attaching under-performing boys to mentor teachers or pupils, involving them in paired reading and preaching to boys about doing better.