ILGA-Europe has around 300 member organisations in 47 European countries.These include national and local organisations, as well as trades union based groups, political party based groups, women's groups, etc. Many of ILGA-Europe's member organisations combine human rights campaigning with the provision to their community of support services such as telephone help lines, HIV information and advice, and counselling.

It is governed by an Executive Board elected by the membership at the annual conference. They, together with the membership, are responsible for the main policies and strategic direction of the organisation. The day-to-day operations of the organisation are managed by the Executive Director, and the management and staff teams of ILGA-Europe.