In May 2004, the IHEU met in Kampala, Uganda for its first General Assembly in Africa, and for a regional conference to inaugurate the African Humanist Alliance. One of the issues discussed at the event was homosexuality.

IHEU was among the organisations represented at the 42nd session of the African Commission on Human and Peoples' Rights(ACHPR) held from November 14th to 30th at Palais du Parlement in Brazzaville, Republic of Congo. This session was organised to mark the 20th anniversary of the Commission.