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{{See also|First Nagorno-Karabakh War}}

The major domestic and international issue affecting Azerbaijan is the dispute over [[Nagorno-Karabakh]], a predominantly ethnic Armenian region within Azerbaijan. The current conflict over Nagorno-Karabakh began in 1988 when ethnic Armenian demonstrations against Azerbaijani rule broke out in both Nagorno-Karabakh and Armenia, and the Nagorno-Karabakh Supreme Soviet voted to secede from Azerbaijan. In 1990, after violent episodes in Nagorno-Karabakh, Baku, and Sumgait, the Soviet Union's Government in Moscow declared a state of emergency in Nagorno-Karabakh, sent troops to the region, and forcibly occupied Baku. In April 1991, Azerbaijani militia and Soviet forces targeted Armenian paramilitaries operating in Nagorno-Karabakh; Moscow also deployed troops to Yerevan. Azerbaijan declared its independence from the U.S.S.R. on August 30, 1991. In September 1991, Moscow declared it would no longer support Azerbaijani military action in Nagorno-Karabakh. Armenian militants then stepped up the violence. In October 1991, a referendum in Nagorno-Karabakh approved independence.

More than 30,000 people were killed in the fighting from 1992 to 1994. In May 1992, Armenian and Karabakhi forces seized Susha (the historical, Azerbaijani-populated capital of Nagorno-Karabakh) and Lachin (thereby linking Nagorno-Karabakh to Armenia). By October 1993, Armenian and Karabakhi forces had succeeded in occupying almost all of Nagorno-Karabakh, Lachin, and large areas in southwestern Azerbaijan. As Armenian and Karabakhi forces advanced, hundreds of thousands of Azerbaijani refugees fled to other parts of Azerbaijan. In 1993, the UN Security Council adopted resolutions calling for the cessation of hostilities, unimpeded access for international humanitarian relief efforts, and the eventual deployment of a peacekeeping force in the region. The UN also called for immediate withdrawal of all ethnic Armenian forces from the occupied territories of Azerbaijan. Fighting continued, however, until May 1994 when Russia brokered a cease-fire.