The party was subject to political violence from drug lords, paramilitaries and security forces agents during the mid-1980s, leading to its eventual decline, virtual disappearance, and extermination.

The peace negotiations with the government gave both the FARC and the new UP a high media profile that the guerrillas and their ideas had never experienced before, appearing in radio, television and newspaper chronicles regularly.

[7] By 1987, the party's leadership began to be gradually but increasingly decimated by the violent attacks and assassinations carried out by drug lords, proto-paramilitary groups and some members of the government's armed forces that acted together with the above, with what many observers consider as the passive tolerance (and in, some instances, the alleged collaboration) of the traditional bipartisan political establishment.

An April 1988 report by Amnesty International charged that members of the Colombian military and government would be involved in what was called a "deliberate policy of political murder" of UP militants and others.

Numerous car bombs and explosives were also regularly activated in several important Colombian cities, including the capital Bogotá, leaving hundreds dead and wounded.

[8] While some investigations were opened and some of the gunmen and military men involved were captured and convicted, most of the murders committed during these years were never resolved and most of those intellectually responsible were never punished, indicating a high degree of judicial impunity that continues to plague modern Colombia.

It has been claimed by some of the individuals responsible, such as the AUC's Carlos Castaño (who published a book in which he admitted his participation in many of these events and has apparently regretted a number of his actions), that they believed that the UP was nothing more than a FARC front, in order to attempt to rationalize the violence.

It is usually an accepted figure to state that allegedly some 2,000 to 3,000 of its members were murdered (the highest unofficial and unconfirmed estimates, irregularly employed by the FARC and a small number of analysts, speak of 5,000 or more).

[11][12] Two presidential candidates were murdered, plus eight congressmen, 70 councilmen, dozens of deputies and mayors, hundreds of trade unionists, communist and peasant leaders, and an unestablished number of militants.

The official legal representatives of a partial number of UP victims presented a concrete death toll of about 1,163 to the Inter-American Commission on Human Rights (IACHR), of which 450 (38%) were attributed directly to paramilitary groups.

Bernardo Jaramillo, a lifelong member of the Communist Party, witnessed the deaths of his comrades and had openly criticized the positions of both the FARC and the Colombian government, because of what he considered as their mutual intolerance and lack of willingness to compromise for peace.

FARC officially considers that the UP's extermination was a clear sign of government intolerance, state terrorism and of the impossibility of legal political action in Colombia.

For these reasons, many are skeptical and highly critical of the demobilization negotiations that Álvaro Uribe's administration is holding with the AUC, because they fear that they might result in undue impunity.

On February 4, 2004, Vice president Francisco Santos announced that the Colombian state had reached an official agreement with the Reiniciar NGO, which represents a number of victims belonging the UP and the Communist Party, who had presented their cases before the IACHR earlier.

[13][18][19] The agreement would mean that the Colombian state has accepted that it is legally obliged to begin to seek a final compromise with the victims, which should provide an investigation of the crimes and judicial sanction for those responsible, in addition to a degree of moral and economic reparation.