Prior to the 2001 invasion of Afghanistan, the Islamic Movement of Uzbekistan (IMU) posed the greatest threat to the Karimov administration. In 2002 the IMU was reclassified as terrorist by the United States. Since the invasion, the IMU has been greatly weakened due to US military actions which cut off its supply of resources and killed its leader, Juma Namangani.

The largest terrorist attacks were the 1999 Tashkent bombings, the IMU invasions of 2000-2001, and the Tashkent attacks of March and July 2004.

After visiting Uzbekistan in 2002 the UN Special Rapporteur on Torture found torture and ill-treatment of prisoners to be systematic. Human Rights Watch estimated in 2004 that there were over 6,000 Uzbeks in prison for practising Islam outside of the state-run religious establishment.

According to HRW, "In addition to hundreds of reports of beatings and numerous accounts of the use of electric shock, temporary suffocation, hanging by the ankles or wrists, removal of fingernails, and punctures with sharp objects, Human Rights Watch received credible reports in 2000 that police sodomized male detainees with bottles, raped them, and beat and burned them in the groin area. Male and female detainees were regularly threatened with rape. Police made such threats in particular against female detainees in the presence of male relatives to force the men to sign self-incriminating statements. Police also regularly threatened to murder detainees or their family members and to place minor children in orphanages. Self-incriminating testimony obtained through torture was routinely admitted by judges, who cited this as evidence, often the only evidence, to convict. Courts did not initiate investigations into allegations of mistreatment by police."

Human rights organizations have detailed the improper "imposition of capital punishment" since Uzbekistan's independence.

On February 16, 1999, six car bombs exploded in Tashkent, killing 16 and injuring more than 100, in what may have been an attempt to assassinate President Islam Karimov. The IMU was blamed.

The Uzbek government agreed on 7 October 2001 to allow US troops and planes to use Uzbekistan's airspace and stay at Karshi-Khanabad airbase, and to convene "urgent" bilateral security talks with the United States if Taliban fighters spread fighting north into Uzbekistan. They agreed in a joint statement to seek to "eliminate international terrorism and its infrastructure. For these purposes, the Republic of Uzbekistan has agreed to provide the use of its airspace and necessary military and civilian infrastructure of one of its airports, which would be used in the first instance for humanitarian purposes." A week earlier Defense Secretary Donald Rumsfeld visited Uzbekistan and met with President Islam Karimov. Karimov agreed to assist the US in the war on terror by lending Karshi-Khanabad for "humanitarian" search and rescue missions. Taliban officials warned the Uzbek government that they would be attacked if they helped in the US invasion. 1,000 US troops were sent to Karshi-Khanabad between Rumsfeld's visit and the second agreement of 7 October. At the same time the Taliban sent 10,000 troops to the Afghanistan-Uzbekistan border. A spokesman for the Uzbek Foreign Ministry said, "Concentrating 10,000 troops on the border would be a dangerous tactic for the Taliban, because they would become targets for US bombing raids." State Department spokesman Richard Boucher said Uzbekistan is "a country that we've worked with for many years in the past to help them with border security, to help them with anti-terrorism efforts and (there are) terrorism and threats coming at them from Afghanistan."

The IMU launched a series of attacks in Tashkent and Bukhara in March and April 2004. Gunmen and female suicide bombers took part in the attacks, which mainly targeted police. The violence killed 33 militants, 10 policemen, and four civilians. The government blamed Hizb ut-Tahrir, though the Islamic Jihad Union (IJU) claimed responsibility.