The crackdown, in turn, fuelled the growth of an insurgency by the Islamic Movement of Uzbekistan (IMU).
The relationship made it uncomfortable for the US and EU to speak out about human rights abuses in Uzbekistan.
At first Uzbekistan had a competitive political system but by 1995 Karimov had eliminated all opposition.
Relations remain strained, even as Uzbekistan serves as a transit hub for the Afghanistan military withdrawal.
Uzbekistan is central Asia's most populous state and strives to assert itself as a regional power.
After 9/11 Uzbekistan became a close strategic partner of the US, providing military facilities and transit routes to support US and Nato operations in Afghanistan.
Welcome to Uzbekistan, a country bigger than Germany, with a population of 31 million, where Islam Karimov is now embarking on a fourth term of office, even though the constitution stipulates a two-term maximum for heads of state.
Related: Thousands jailed in Uzbekistan on politically motivated charges, report says Human rights groups also lambasted the election as unconstitutional and unfair, while also noting the Karimov regime's track record of abuses and repression of criticism.
Islam Karimov, a Communist party boss during the Soviet era, has led Uzbekistan since independence in 1991.
Related: Islam Karimov set to reprise presidential role as Uzbekistan heads to the polls This will be his third term under the current constitution, even though that same treaty limits presidents to two terms, an Organisation for Security and Cooperation in Europe observer mission noted in a report.
Last month the US department of labor reported that Uzbekistan had made "no advancement" in eliminating the worst forms of child labour, although the International Labor Organization ILOO) has noted tentative progress.
