[16] In 1983, he was a member of the group of army officers who backed Defence Minister Óscar Mejía's coup d'état against de facto president Efraín Ríos Montt.

[22] He was the candidate of the Patriotic Party in the 2007 presidential election, campaigning under the slogan "Mano dura, cabeza y corazón" ("Firm hand, head and heart"), advocating a hard-line approach to rising crime in the country.

After receiving the second-largest number of votes in the initial contest on 9 September, he lost the election to Álvaro Colom of the National Unity of Hope in the second round on 4 November 2007.

Victims included Aura Marina Salazar Cutzal, an indigenous woman who was secretary to the party's congressional delegation and an assistant to Pérez.

[29] Vice President Alejandro Maldonado Aguirre was appointed to serve the remainder of Pérez's 4-year term in office (due to end on 14 January 2016).

[31] On 27 October 2017,[32] Judge Miguel Ángel Gálvez of Guatemala City ordered Pérez, Baldetti, and another 26 people, including former senior officials from Guatemala's customs duty system, to stand trial on charges related to bribes channeled to officials helping businesses evade customs duties and Pérez has remained in custody since his 2015 arrest.

[35] In 2011, reports were made, based on the United States' National Security Archives, that Pérez was involved in the scorched earth campaigns of the 1980s under the military dictator Efraín Ríos Montt.

[36] Pérez commanded a counterinsurgency team in the Ixil Community in 1982-3 and is accused of ordering the mass murder of civilians, destruction of villages, and resettlement of the remaining population in army-controlled areas.

[39][40] In July 2011, the indigenous organization Waqib Kej presented a letter to the United Nations accusing Pérez of involvement in genocide and torture committed in Quiché during the civil war.

His wife, American lawyer Jennifer Harbury, has presented evidence that Pérez, who was Director of Military Intelligence at the time, probably issued the orders to detain and torture the commandant.

American journalist Francisco Goldman argues that Pérez Molina may have been present, along with two other high officials, a few blocks from the April 1998 murder of Juan José Gerardi Conedera, a Roman Catholic bishop.

[51] Gerardi was murdered two days after the release of a human rights report he helped prepare for the United Nations' Historical Clarification Commission.

[53] The same day, a woman named Patricia Castellanos Fuentes de Aguilar was shot and killed after meeting with Pérez's wife, Rosa María Leal.