The Yale University study found that lesbian and bisexual girls were particularly at risk. They were two to three times more likely to be punished than straight girls for the same misconduct.
Researchers said that while there were substantial differences in the arrests, police stops, convictions and school expulsions of gay and straight teenagers, there was no evidence for differences in behaviour.
Teenagers who identified as lesbian, gay or bisexual or said they had once had same-sex attraction or a same-sex relationship were 40 per cent more likely than their straight peers to be convicted of a crime as adults.
They were between 30 and 50 per cent more likely to be stopped by the police and more likely to be expelled from school. Ten per cent of the LGB teenagers surveyed said they had been expelled, compared to seven per cent of heterosexual respondents.
Kathryn Himmelstein, lead author of the study, published in the journal Pediatrics, said that while the evidence that LGB teens are punished more severely is clear, the reason why this happens is not.
It’s definitely troubling to see such a disparity,” she told the Washington Post.
“It may very well be not intentional. I think most people who work with youth want to do the best they can for young people and treat them fairly, but our findings show that’s not happening.”
Girls who identified as lesbian or bisexual were 50 per cent more likely than straight girls to be stopped by the police for the same behaviour and had twice as many arrests and convictions.
Ms Himmelstein commented that this could be due to bias towards women who subvert feminine norms by dressing or behaving in more masculine ways.
The study used data from the National Longitudinal Study of Adolescent Health, which followed 15,000 middle and high school students between 1994 and 2002. Researchers said they expected findings to remain applicable to date.
Researchers studied the experiences of 1,500 students who said they were lesbian, gay or bisexual and 2,300 who reported having same-sex attraction at some point.
Media attention on LGBT suicides and anti-gay bullying has intensified over the past few months after a spate of reported suicides among teenagers known or thought to be LGBT.