Fewer than one in 10 gays and lesbians come out by the time they reach 16 and the later they do the greater the risk of emotional and mental health problems.
Moray Paterson, a health promotion specialist with gay and lesbian young people in Lothians, told a seminar at the educational psychologists'
conference at Heriot-Watt University that homophobic bullying was commonplace in schools.
Physical education classes were often associated with such bullying and many young people did not want to take part. One PE teacher had told a pupil to stop "mincing about", a put-down that was unacceptable in the language of equality.
"Language is the biggest barrier in this work," Mr Paterson said. "People do not want to say the wrong thing and sometimes just don't say anything."
A more liberal climate in which the age of consent had been lowered to 16 was an indicator of the improvement in attitudes in the 23 years since homosexuality was decriminalised in Scotland. But young people in school still needed information and support.
Liz McIntyre, a psychologist in Dumfries and Galloway who is carrying out research in Scottish schools, described the issue as "invisible and silent". Her son had come out at the age of 18. He, too, had hated PE and sport and had preferred mixing with girls and activities like sewing.
The two areas of society not prepared for young people to come out were schools and families. Young people did not want to disappoint their parents and were worried about their reaction.
Mrs McIntyre said there was a paucity of research on sexuality, particularly on lesbian girls. Most was on gay boys. "What the research says is that these youngsters tend to be more sensitive, tend to cry more and tend to like more aesthetic activities, like music and nature.
"About 11 years of age is when these youngsters start to feel homoerotic feelings. But very quickly they cannot consolidate these kind of feelings and very quickly they realise they are condemned. They are confused about it naturally and sometimes start to hate themselves."
In the longer term, young people could skip school, let their work slide, move towards self-harm and suffer post-traumatic stress disorder.
Schools, however, found it difficult to face up to homosexuality. A male primary teacher told Mrs McIntyre he feared for his job if he raised the issue. The teacher said: "To bring the word gay up or even a short discussion using the word, it would go back to parents through the children."
Mrs McIntyre said teaching about sexuality was entirely from the heterosexual stance and even school dances assumed everyone was heterosexual. It was time for the Scottish Executive to tackle the issue given its commitment to social inclusion and equality.