His research focuses on the role of the Vatican, Swiss authorities and the government of Argentina in organizing "ratlines"—escape routes for Nazi criminals and collaborators.

[2] Drawing on investigations in Argentine, Swiss, American, British, and Belgian government archives, as well as numerous interviews and other sources, Goñi's conclusions are detailed extensively in The Real Odessa: Smuggling the Nazis to Perón's Argentina[a] and several follow-up books.

He also wrote an article for The Guardian in which scientific testing on a skull fragment put into question the authenticity of mainstream accounts of the death of Adolf Hitler.

[5] Following publication of the book in Italy, a group of parliamentarians in Rome demanded that Prime Minister Berlusconi open an investigation into the passage of Nazis through their country.

[11] He is also the author of two previous books in Spanish, El infiltrado, la verdadera historia de Alfredo Astiz,[b] regarding crimes committed by Argentina's 1976–83 military dictatorship, and Perón y los alemanes,[c] on wartime links between Berlin and Buenos Aires.