The online survey questioned around 93,000 people in the European Union's 27 member states, plus Croatia. It found many experienced homophobia, bullying, physical violence or were afraid to display their sexuality in public.
According to the findings, more than a quarter (26 percent) said they had been physically or verbally assaulted over the last five years, and 47 percent said they had been harassed in the past 12 months. Many believed the most recent incident happened because of their sexual orientation or gender identity.
Around 80 percent said they did not go to the police after an attack, or were afraid to do so, believing their cases would not be dealt with.
The European Union's Agency for Fundamental Rights (FRA), which conducted the poll, said discrimination towards sexual minorities was commonplace, and could occur in seemingly everyday situations, such as going to sports clubs and hospitals, going out at night, dealing with banks or looking for an apartment.
"The results of the FRA survey show LGBT people experience fear, isolation and discrimination on a daily basis in Europe," said the FRA director, Morten Kjaerum. The FRA said the survey was the largest-ever on LGBT hate crime and discrimination.
Just under a third of transgender people said they had been victims of violence. The report said those whose identity or appearance did not match their physical gender faced the highest rate of discrimination, including at their place of employment or health services.
The study also ranked perceived discrimination by country, with the Netherlands having the lowest rate at 30 percent. The Netherlands was the first country in the world to legalize same-sex marriage, in 2001. More than 60 percent of those surveyed in Croatia, Romania and Lithuania said they felt disadvantaged in areas like healthcare, work and education.
The FRA said discrimination often began at school, with two out of three LGBT respondents hiding their sexual orientation. More than 80 percent of respondents in every EU member state said they could recall negative comments or bullying of LGBT youth at school.
"Member states must take care that LGBT students feel secure at school, given that that is where LGBT people's negative experiences, social prejudice and exclusion often begins," the FRA said.
The report was released on the International Day Against Homophobia.
jr/msh (AFP, dpa)