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In many cases there was no intervention from pupils, teachers or other staff.
The research in Dumfries and Galloway has prompted a call for more to be done to tackle discriminatory language.
LGBT Youth Scotland said it was clear action was required. The EIS union said teachers used a range of approaches to deal with such issues.
The research received responses from nearly 400 pupils across the region.
Kerry Riddell of LGBT Youth Scotland said it was an issue that could have serious repercussions for the students involved.
“It is a really big concern,” she said. “We know that if a young person hears negative comments relentlessly about their identity, it is not particularly good for your mental health.
“It doesn’t encourage you to come out if that’s something that you were considering doing.
“Being in the closet for many years is not good for your mental health either so there’s a real impact of that kind of relentless negative language that people hear.”
She said a lot of the young people using discriminatory terms did not do it out of “badness”.
“They just need to understand a bit more about the impact of it and that’s really where professionals come in,” she said.
“There is certainly more work to be done in schools to tackle it.”