Two-fifths of LGBT people considered themselves to have mental health problems, a survey of 350 LGBT Youth Scotland respondents aged 13 to 25 found.
This is higher than general estimates that one in four people in Scotland will have mental health problems at some point in their life.
Mental health problems appear to be much higher among transgender people (66%), based on responses from around 35 people.
Lesbians were more likely (44%) to feel mentally ill than gay men (27%), based on around 230 respondents.
Bisexual women were over three times as likely (63%) than bisexual men (20%) to feel mentally ill, based on around 56 respondents.
Two-fifths who experienced homophobic or biphobic bullying in education and over two-thirds who experienced transphobic bullying felt mentally ill.
LGBT Youth said: "These results indicate the majority of LGB young women and transgender young people do not feel safe and supported by the NHS. More needs to be done to support lesbian, gay and bisexual young women and transgender young people in relation to their mental health."
Over half (56.5%) of LGBT young people said they felt safe and supported by the NHS, but this was lower for LGBT women (43.1%) and transgender people (48.1%).
LGBT people are significantly more likely to shun religion with 73% indicating no faith, compared with 43% of the general population, although 15% indicated a Christian faith and small numbers said Buddhist, Jewish, Muslim and other.