Conflict in northern Uganda
President Museveni offered to grant amnesty to the top five LRA leaders, including Joseph Kony and Raska Lukwiya, if a peace deal was reached. This was despite arrest warrants against them for crimes against humanity and war crimes issued by the International Criminal Court (ICC) in 2005.
A series of talks between the government and the LRA took place from July, sponsored by the government of Southern Sudan.
On 1 August, Joseph Kony called for a truce. Raska Lukwiya was killed in battle on 12 August.
The government and the LRA agreed a ceasefire on 26 August. Under its terms, LRA forces were to gather in two areas in Southern Sudan. By mid-September LRA fighters had started gathering at the assembly areas in Southern Sudan, but they subsequently left, fearing attack by the Uganda People's Defence Force (UPDF).
On 2 September President Museveni asked the ICC to maintain the charges against the LRA until a comprehensive peace agreement was reached, but said that once this was agreed the government would intervene to keep the commanders "safe" from the ICC. Late in September, peace talks stalled over the issue of the ICC warrants, and in October the UPDF said it had resumed its offensive against LRA rebels who had failed to assemble in the required areas.
Despite breaches of the ceasefire, in November both sides agreed to prolong it and talks continued.
As the peace process continued, a number of confidence building measures took place from November with the government facilitating visits by family members of the LRA leadership and by community leaders from northern Uganda for consultations with the LRA leaders.
AI condemned the offer of amnesty made by President Museveni to the LRA leaders and stated that the offer of "protection" was in violation of Uganda's obligations under international law, since it itself referred the cases to the ICC on the basis that national authorities were unable to deliver justice for crimes committed in northern Uganda.
Internally displaced people
There were 1.7 million internally displaced people in the north, most in camps or settlements around villages. Conditions in camps were poor, with high mortality rates as a result of malnutrition, lack of sanitation and insecurity.
After the ceasefire, some people began returning home and the government set a deadline of 31 December to clear the camps. A number of sites were identified as suitable for resettlement and by October UN officials estimated that more than 300,000 people had left the camps.
Refugees in Uganda
In March the government passed a new refugee bill incorporating provisions of international refugee law.
In March the Ugandan and Southern Sudanese governments signed an agreement to repatriate Sudanese refugees. In July, the UN refugee agency UNHCR announced that 10,000 refugees had returned.
Some Congolese refugees returned to the Democratic Republic of the Congo (DRC) early in 2006, but further insecurity in the DRC prompted new arrivals of refugees.
Attacks on freedom of expression
Attacks on freedom of expression and press freedom continued, in particular during the election campaign. The police intervened to prevent programmes relating to the presidential candidates being aired, and several journalists were arrested during the run-up to the election. Radio stations were banned from broadcasting any debate or programme about Dr Besigye's trial.
• On 23 February, police stormed Radio Pacis and stopped a talk show featuring the FDC deputy secretary general Kassiano Wadri.