- The conquest of Mesoamerica by Spain in the name of the Church
- The legal process on the Italian scientist and philosopher Galileo Galilei, himself a devout Catholic, around 1633 (31 October 1992).
- Catholics' involvement with the African slave trade (9 August 1993).
- The Church Hierarchy's role in burnings at the stake and the religious wars that followed the Protestant Reformation (May 1995, in the Czech Republic).
- The injustices committed against women, the violation of women's rights and for the historical denigration of women (10 July 1995, in a letter to "every woman").
- The inactivity and silence of many Catholics during the Holocaust (see the article Religion in Nazi Germany) (16 March 1998)
- For the execution of Jan Hus in 1415 (18 December 1999 in Prague). When John Paul II visited Prague in 1990s, he requested experts in this matter "to define with greater clarity the position held by Jan Hus among the Church's reformers, and acknowledged that "independently of the theological convictions he defended, Hus cannot be denied integrity in his personal life and commitment to the nation's moral education." It was another step in building a bridge between Catholics and Protestants.
- For the sins of Catholics throughout the ages for violating "the rights of ethnic groups and peoples, and [for showing] contempt for their cultures and religious traditions". (12 March 2000, during a public Mass of Pardons).
- For the sins of the Crusader attack on Constantinople in 1204. (4 May 2001, to the Patriarch of Constantinople).
Though he called on all Catholics to follow his example, the Philippine Catholic Church has pridefully and sinfully denied him--for where is the apology for the conquest of the Philippines by Magellan and Legaspi in the name of King and Cross? And where the apology for the dastardly murder of Jose Rizal using the testimony and evidence supplied by his own Jesuit mentors?