"Fear, isolation and discrimination are everyday phenomena for the LGBT community in Europe," the director of the European Union's Agency for Fundamental Rights (FRA), Morten Kjaerum, wrote in the report.
The online survey, described as the largest of its kind, questioned around 93,000 people in the European Union's 27 member states plus Croatia, which is to join the bloc in July.
Over a quarter (26 percent) of the respondents said that they had been physically or verbally assaulted over the last five years.
Some respondents said that attitudes were worsening, even in countries that are traditionally considered to be tolerant.
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"My situations of harassment/discrimination/violence are mainly random acts of verbal aggression," a 27-year-old gay Belgian wrote.
"The situation is worse now than it was, for example, four years ago."
In The Netherlands, the first country in the world to legalise gay marriage in 2001, almost 20 percent of those taking part said they felt discriminated against when going to sport clubs or hospitals, looking for an apartment, going out at night, or dealing with banks.
"(I am) reluctant to report anything that might indicate that I am gay, as I know (the police) just dismiss everything," a 42-year-old Frenchman said.
Two-thirds of respondents and three-quarters of gay men said they were afraid to show their sexuality in public.
The FRA report noted that discrimination often begins at school, where two-thirds of respondents hid their sexual orientation.
"Ten years later, I still consider being bullied at school the worst form of homophobic abuse I've ever been subjected to," said a gay Maltese man, 25.