A quarter of gay people surveyed in a major EU poll say they have been subjected to attacks or violent threats in the past five years, BBC reported.
Poorer and younger respondents were more likely to face discrimination due to their sexuality, the survey found.
Some 93,000 people in the EU and Croatia were polled in the EU's first survey on this scale.
Gay rights campaigners welcomed the report but called for stronger legal action by Brussels to tackle the issue.
Ilga-Europe, a non-governmental organisation which surveys attitudes to gay issues, told the BBC it regretted that a comprehensive EU Anti-Discrimination Directive drafted by the European Commission in 2008 had yet to be approved by EU leaders.
Ilga's own annual report published on Thursday found "little legislative progress towards protecting LGBTI [Lesbian, Gay, Bisexual, Transgender/Transexual and Intersexed people] from discrimination in accessing goods and services".
In a survey ranging across both the EU and the rest on Europe, the NGO noted the hostility gay people encountered in former Soviet states like Russia and Georgia when they tried to demonstrate publicly.
On Friday, about 10,000 anti-gay protesters in the Georgian capital Tbilisi stormed police barricades, beating and chasing a couple of dozen gay activists who had tried to mark the international day against homophobia.