On 29 February 2016, Guterres submitted his nomination as Portugal's candidate for the 2016 UN Secretary-General selection.
The UN's role in the Haiti cholera outbreak has been widely discussed and criticized after Ban ki-moon administration denied the issue for several months. According to the Boston-based Institute for Justice & Democracy in Haiti, the UN is the proximate cause for bringing cholera to Haiti. Peacekeepers sent to Haiti from Nepal were carrying asymptomatic cholera and they did not treat their waste properly before dumping it into Haiti's water stream. During his UNSG informal dialogue, Jamaica, on behalf of the Caribbean Community, asked if the UN should assume liability for any deaths within local populations that result from the introduction of infectious disease by its peacekeepers. Jamaica also asked if Guterres believes compensation should be provided. Gueterres responded by calling the situation a "particularly complex question." He says that it is difficult to preserve diplomatic immunity while also ensuring there is no impunity, but that he would "pay a lot of attention in trying to find the right equilibrium between these two aspects that are absolutely crucial."
Another issue that has been brought up is the sexual exploitation and abuse by UN peacekeepers. This gross problem was brought to light after Anders Kompass exposed the sexual assault of children by peacekeepers in the Central African Republic and, as a consequence, dismissed by Ban Ki-moon administration before being rehabilitated in court.During the United Nations Secretary General Candidate informal dialogues, Guterres indicated it was completely unacceptable that there be UN forces committing human rights violations such as rape and sexual violence. "All of us together—states and UN—must do our utmost to ensure that any kind of action of this type is severely punished," remarked Guterres.The United States raised the question of international tribunals to try peacekeepers for their crimes. Guterres responded by saying an independent jurisdiction would be excellent but that "the only way to get there is through a new compact with all key parties true contributors, financial contributors, and to make sure that there is an adjustment in the relation between countries the UN and the support those that are contributing with troops receive in order to be able to do it much better."He also indicated that there is a gap between theoretical zero-tolerance and the ineffective zero-tolerance that actually exists on the ground that needs to be overcome.
On 5 October 2016, the 15-member United Nations Security Council announced that they had agreed to nominate Guterres, after an informal secret ballot in which he gained 13 encourage votes and two no opinion votes. Runner-up Kristalina Georgieva, officially supported by Germany, had 8 discouraging votes. The UNSC will officially nominate Guterres, by adopting a formal resolution on 6 October, which must then be also adopted by the United Nations General Assembly. Guterres is due to take office on 1 January 2017.