Prisoners of conscience were among hundreds of political prisoners arrested during the year, scores of whom were detained incommunicado in unofficial places of detention. Serious charges that preclude bail for statutory periods were used to hold more than 200 prisoners without trial. Hundreds of political and criminal prisoners were tortured. Soldiers were allegedly responsible for dozens of rapes. Courts imposed the cruel, inhuman and degrading punishment of caning. Four men apparently wanted by neighbouring states "disappeared". Soldiers and police were responsible for more than 40 possible extrajudicial executions, including of children. At least 21 prisoners were sentenced to death. Armed opposition groups were responsible for gross human rights abuses, including child abduction, beatings, rape and deliberate and arbitrary killings.

Bomb attacks in March, April and July in and around Kampala marked the extension to the capital of wars involving armed opposition movements operating out of the Democratic Republic of the Congo (DRC) with the support of the Sudanese government. In August President Yoweri Museveni ordered troops into the DRC in support of a rebellion by the Congolese armed opposition group, the Rassemblement Congolais pour la démocratie (RCD), the Congolese Rally for Democracy. In response, the Sudanese government airlifted soldiers from Ugandan armed opposition groups based in Sudan to the DRC as part of a troop deployment in support of DRC President Laurent-Désiré Kabila. Also in August there were bomb threats against the US Embassy and other targets in Kampala immediately after the bombing of the US Embassies in the Kenyan capital Nairobi and the Tanzanian capital Dar es Salaam. The authorities blamed some of the threats on Ugandan armed opposition movements. Before the end of the month three buses leaving Kampala were bombed, killing 28 people. In this tense political climate, intensified activity by security agencies often breached international human rights standards and Ugandan constitutional provisions.

Fighting in the west, north and northwest between the government's Uganda People's Defence Forces (UPDF) and armed opposition groups continued throughout the year. In the west the Allied Democratic Front (ADF) was active in districts bordering the Rwenzori mountains on the frontier with the DRC. In the north, fighting between the UPDF and the armed opposition Lord's Resistance Army (LRA) displaced approximately 30,000 people in Kitgum District early in the year. The LRA extended its operations to Lira District and, briefly, as far east as Soroti; over 15,000 people were displaced in Lira. LRA bases in Sudan were overrun by the Sudan People's Liberation Army (SPLA) supported by UPDF troops in September. However, within a few weeks the Sudanese army had dislodged the SPLA and UPDF, and in November an LRA unit crossed into Uganda from Sudan and renewed military operations in Kitgum. Armed opposition groups in northwest Uganda regrouped after defeats in early 1997; the Uganda National Rescue Front II (UNRF-II) renewed activity in March 1998 and the West Nile Bank Front (WNBF) began incursions from bases in the DRC in June.

Over 400,000 people remained internally displaced in Gulu and Kitgum Districts in the north. Many expressed the wish to return to their villages but were not allowed to by the UPDF. In western Uganda at least 15,000 people were displaced in April, but tens of thousands who fled their homes in 1997 were able to return home.

In April the UN Commission on Human Rights adopted a resolution condemning the abduction of children by the LRA and calling on member states, international organizations, humanitarian bodies and others to exert pressure on the armed group to release children.

In July the Uganda Human Rights Commission published its first annual report, covering 1997. It identified human rights violations by the state and reported that despite the Commission's constitutional status, on some occasions state institutions had failed to cooperate fully with it.

Prisoners of conscience were among hundreds of political prisoners arrested during the year, scores of whom were detained incommunicado in secret detention centres. Muslims were particularly targeted. Prisoners of conscience included members of the Ugandan Somali community detained outside the law in September. Omer Ahmed Mandela, treasurer of the popular Kampala football club S.C. Villa, Sheikh Abdul Weli Abdullai, imam of the Tawheed mosque, and 27 men and boys were arrested by security officials and by agents from the US Federal Bureau of Investigation. Questioned about the bombing of the US Embassy in Nairobi and alleged plans to bomb US targets in Uganda, they were held incommunicado in a secret place of detention. Most were released without charge after two weeks. However, Abdul Kadir Ali, a 15-year-old school student, and three men were not released until mid-October, again without charge.

Over 100 Muslim political prisoners, the majority from the Islamist Jumaiyat Da'awa Salafiyya sect, were arrested in Kampala and other places in south and west Uganda on suspicion of involvement with the ADF and other armed opposition movements. For example, 40 men detained in Kampala in May, including Sheikh Abdul Karim Sentamu, a senior imam of the sect, were held incommunicado at unknown locations – they effectively "disappeared". In June the Uganda Human Rights Commission publicly ordered their release because their detention was illegal. One of the men arrested in May was known to be among 50 men charged with treason in June. However, most remained in incommunicado detention without charge or trial. There were further detentions of Muslims in July and August. Although some were released, at least 14 and possibly many more were still detained at the end of the year.

The authorities continued to use serious charges that preclude the granting of bail for statutory periods as a way of holding political prisoners without trial. On several occasions prisoners who were granted bail at the end of a statutory remand period were rearrested on new serious charges as they left the court. In March, 87 alleged members of the WNBF were rearrested and charged with murder after they were granted bail at the end of a mandatory 360-day remand period on treason charges. In July treason charges were withdrawn against 110 other prisoners held since 1995. They were released but were almost immediately rearrested on new treason charges.

Torture and cruel, inhuman and degrading treatment remained endemic in police stations and was common when soldiers and security officials detained security suspects. At least five prisoners died reportedly after being tortured. In June more than 100 uncharged detainees suspected of collaborating with the ADF were freed from military barracks in Kasese; the newly deployed UPDF commander said that many had been tortured by being beaten and burned with molten plastic. Security suspects held incommunicado in Kampala were also brutally treated. In August detainees held in an illegal secret location by the Directorate of Military Intelligence on suspicion of involvement with the bombing of the US Embassy in Nairobi or of links with the ADF were reportedly beaten and tortured with electric shocks.

Soldiers deployed in rural areas in northern and eastern Uganda were said to have been responsible for dozens of rapes. In July soldiers deployed north of Mbale detained and allegedly raped a number of women, including two who were pregnant. After protests by local councillors an officer and several soldiers were arrested.

Courts imposed the cruel, inhuman and degrading punishment of caning, often for sexual offences. In March, for example, a man convicted of rape was sentenced to 12 strokes and 12 years in jail.

In February, four men – two Rwandese, a Congolese and a Ugandan of Rwandese origin – apparently wanted by neighbouring states "disappeared" after being arrested, continuing a pattern established in previous years. Their fate remained unknown at the end of the year. The Uganda Human Rights Commission said that it believed police officers and officials in the Office of the President were responsible for the "disappearances".

Soldiers and police were responsible for at least 40 killings that appeared to be extrajudicial executions. For example, in January, three prisoners in Luwero were shot dead by police officers who had taken them into the countryside, ostensibly to recover abandoned arms. In May, three alleged armed robbers were shot dead in Gulu. In both cases the police claimed that the prisoners were trying to escape. In March at least 30 children recently abducted by the LRA and bound together were killed by soldiers in circumstances that amounted to an extrajudicial execution at Wang Alur swamp in Kitgum District. In May, soldiers killed Oyet David after he left a camp for the internally displaced near Gulu and returned to his village. Captured by UPDF soldiers, he was reportedly made to lie face down and shot through the head.

The High Court sentenced at least 21 people to death. The sentences against five others were confirmed by the Supreme Court. In the condemned section of Luzira Prison in May there were 112 civilian prisoners whose appeals against the death penalty had been dismissed in previous years and 60 UPDF soldiers who had not been able to appeal because a military appeal court had not been convened. There were no executions.

Armed opposition movements were responsible for gross human rights abuses, including the abduction of children, beatings, rape, sexual slavery and deliberate and arbitrary killings. The LRA abducted hundreds of boys and girls to become soldiers and sexual slaves in Gulu, Kitgum and neighbouring districts such as Soroti. According to escaped children, new captives were beaten or made to kill others. In July, 30 exhausted child captives unable to keep up with an LRA unit heading towards bases in Sudan were reportedly clubbed to death in the Agoro hills in Kitgum. Camps for the internally displaced were attacked to force people to move out of them. Scores of civilians, many of them relatives of local councillors or government officials, were captured and then killed.

Other armed opposition groups also abducted villagers as a method of forced conscription. For example, in June the UNRF-II abducted more than 100 adults and children in Aringa County in the northwest; over 60 escaped or were freed by the UPDF. In August the WNBF abducted over 200 villagers in raids on Koboko and Aringa; 50 escaped.

In western Uganda the ADF abducted several hundred adults and children and unlawfully killed scores of villagers. In February, five civilians were beheaded after their car was stopped at an impromptu ADF roadblock. In June over 70 students were reported to have been deliberately burned alive at Kichwamba Technical College. More than 80 others were abducted and taken to bases inside the DRC.

Amnesty International expressed grave concern at the detention without charge or trial of political prisoners. In May an Amnesty International delegation visited northern Uganda to research human rights abuses in the context of the armed conflict in the north. In meetings with civilian and military officials, the organization raised concerns about the failure to complete legal action against soldiers arrested for alleged human rights violations. In June the organization called on LRA leaders to end their policy of abducting children. In an address in July to the Kacoke Madit, a gathering of Acholi from inside and outside Uganda that brought together government ministers, local officials and government opponents, Amnesty International said that establishing respect for human rights was part of the process of creating the conditions for peace. The organization called on all parties in the northern war to ensure accountability for human rights abuses.

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