He served as a member of the Supreme Court of Argentina from 2003 until 2015, when he resigned due to age restrictions to hold the position.

Then he was the General Director of the Instituto Latinoamericano de Prevención del Delito, a branch of the United Nations.

In 2000, he was assigned by then President Fernando de la Rua as intervenor of the National Institute Against Discrimination, Xenophobia and Racism (INADI).

He is a member of the Crimes Against Humanity Initiative Advisory Council, a project of the Whitney R. Harris World Law Institute at Washington University School of Law in St. Louis to establish the world’s first treaty on the prevention and punishment of crimes against humanity.

A NGO called "La Alameda" brought a lawsuit against Zaffaroni on the basis of him having 6 apartments where prostitution was illegally practiced.