On 14 July 2008, the Chief Prosecutor of the International Criminal Court (ICC), Luis Moreno Ocampo, alleged that al-Bashir bore individual criminal responsibility for genocide, crimes against humanity and war crimes committed since 2003 in Darfur. The prosecutor accused al-Bashir of having "masterminded and implemented" a plan to destroy the three main ethnic groups, the Fur, Masalit and Zaghawa, with a campaign of murder, rape and deportation. The arrest warrant is supported by NATO, the Genocide Intervention Network, and Amnesty International.
An arrest warrant for al-Bashir was issued on 4 March 2009 by a Pre-Trial chamber composed of judges Akua Kuenyehia of Ghana, Anita Usacka of Latvia, and Sylvia Steiner of Brazil indicting him on five counts of crimes against humanity (murder, extermination, forcible transfer, torture and rape) and two counts of war crimes (pillaging and intentionally directing attacks against civilians). The court ruled that there was insufficient evidence to prosecute him for genocide. However, one of the three judges wrote a dissenting opinion arguing that there were "reasonable grounds to believe that Omar Al Bashir has committed the crime of genocide".
International Criminal Court Prosecutor Luis Moreno-Ocampo told U.S. State Department officials on March 20, 2009 that President Bashir 'needed to be isolated.' Ocampo suggested if Bashir’s stash of money were disclosed (he put the figure at possibly $9 billion), it would change Sudanese public opinion from him being a “crusader” to that of a thief.
Sudan is not a state party to the Rome Statute establishing the ICC, and thus claims that it does not have to execute the warrant. However, United Nations Security Council Resolution 1593 (2005) requires Sudan to cooperate with the ICC, and therefore the ICC, Amnesty International and others insist that Sudan must comply with the arrest warrant of the International Criminal Court. Amnesty International stated that al-Bashir must turn himself in to face the charges, and that the Sudanese authorities must detain him and turn him over to the ICC if he refuses.
Al-Bashir is the first sitting head of state ever indicted by the ICC. However, the Arab League and the African Union condemned the warrant. Al-Bashir has since visited Egypt and Qatar. Both countries refused to arrest him and surrender him to the ICC upon arrival. ICC member state Chad also refused to arrest al-Bashir during a state visit in July 2010. Luis Moreno Ocampo and Amnesty International claimed that al-Bashir's plane could be intercepted in International Airspace. Sudan announced that the presidential plane would always be escorted by fighter jets of the Sudanese Air Force to prevent his arrest.
The charges against President al-Bashir have been strongly rejected. Former president of Libya and former Chairman of the African Union Muammar al-Gaddafi characterized the indictment as a form of terrorism. He also believes that the warrant is an attempt "by (the west) to recolonise their former colonies." Egypt said, it was "greatly disturbed" by the ICC decision and called for an emergency meeting of the UN security council to defer the arrest warrant. The Arab League Secretary-General Amr Moussa expressed that the organization emphasizes its solidarity with Sudan. The ICC warrant was condemned for "undermining the unity and stability of Sudan". The Organization of the Islamic Conference denounced the warrant as unwarranted and totally unacceptable. It was argued that the warrant demonstrates selectivity and double standards with concern to war crimes. There have been large demonstrations by Sudanese people supporting President Bashir and opposing the ICC charges. Others argue the warrant sets a dangerous precedent in international relations and could hamper efforts to bring peace to Sudan.
Al-Bashir has rejected the charges, saying "Whoever has visited Darfur, met officials and discovered their ethnicities and tribes ... will know that all of these things are lies." He described the charges as "not worth the ink they are written in". The warrant will be delivered to the Sudanese government, which has stated that it will not carry it out.
The Sudanese government retaliated against the warrant by expelling a number of international aid agencies, including Oxfam and Mercy Corps. President Bashir described the aid agencies as thieves who take "99 percent of the budget for humanitarian work themselves, giving the people of Darfur 1 percent" and as spies in the work of foreign regimes. Bashir promised that national agencies will provide aid to Darfur.
During a visit to Egypt, al-Bashir was not arrested, leading to condemnation by Amnesty International. In October 2009 al-Bashir was invited to Uganda by President Yoweri Museveni for an African Union meeting in Kampala, but did not attend after protest by several NGOs. On October 23, 2009, al-Bashir was invited to Nigeria by President Umaru Yar'Adua for another AU meeting, and was not arrested. In November, he was invited to Turkey for an OIC meeting. Later, he was invited to Denmark to attend conferences on climate change in Copenhagen.
It is alleged that by holding and winning legitimate presidential elections in 2010, al-Bashir hoped to evade the ICC warrant.
Al-Bashir was one of the candidates in the 2010 Sudanese presidential election, the first democratic election with multiple political parties participating in decades. On April 26, he was officially declared the winner after Sudan's election commission announced Bashir received 68% of the votes. However, "the voting was marred by boycotts and reports of intimidation and widespread fraud."
Al-Bashir also visited Kenya on 27 August 2010 to witness the President signing Kenya's new constitution into law.
On May 8, 2011, al-Bashir visited Djibouti to attend the inauguration of President Guelleh's third term.
In June 2011, China's president Hu received al-Bashir as 'friend and brother' in Beijing, fostering China's interests in Sudan's resources.
Bashir was received in Libya along with a high-level delegation on the 7th January 2012 in a bid to restore friendly relations and offer support to the new Libyan government after the fall of Gaddafi.
The initial ICC charges against al-Bashir, which included seven counts of crimes against humanity and war crimes, were issued in March 2009 but did not include genocide counts. On appeal, the lower court was found by appellate judge Erkki Kourula to have erred in law and was ordered to reexamine the evidence for genocide. Prosecutor Luis Moreno Ocampo anticipated that the reexamination could lead to charges within four to twelve months. Then, on February 3, 2010, the judges at the International Criminal Court held that the Pre-Trial Chamber had improperly dismissed the genocide charges against al-Bashir and ordered the Pre-Trial Chamber to reconsider them.
On July 12, 2010, the Pre-Trial Chamber applied the standard of evidence stated by the appellate court, and held that there was sufficient evidence to issue a second arrest warrant for the crime of genocide. A second arrest warrant for President al-Bashir was later issued with three added counts of genocide. The new warrant included the Court's conclusion that:
"There are reasonable grounds to believe that (Omar al-Bashir) acted with specific intent to destroy in part the Fur, Masalit and Zaghawa ethnic groups in the troubled Darfur region".
The ICC released a further statement saying that al-Bashir's charges now include "genocide by killing, genocide by causing serious bodily or mental harm and genocide by deliberately inflicting on each target group conditions of life calculated to bring about the group's physical destruction" in three separate counts. The new warrant will act as a supplement to the first, whereby the charges initially brought against al-Bashir will all remain in place, but will now include the crime of genocide which was ruled out initially, pending appeal.
On 28 August 2010 in Nairobi, Kenya chose not to arrest Sudanese President Omar Hassan al-Bashir on International Criminal Court (ICC) charges of genocide when he arrived on Friday for a ceremony for the East African nation’s new constitution. He was escorted into Nairobi’s Uhuru Park, where the signing ceremony was taking place, by Tourism minister Najib Balala. On 28 November 2011, Kenya's High Court Judge Nicholas Ombija ordered the Minister of Internal Security to arrest al-Bashir, "should he set foot in Kenya in the future".