He has expressed support for recreating the Soviet Union.
Khudoiberdiyev helped President Rakhmonov become head of state in 1992, but began a rebellion on 16 August 1997. Two days later reports of Uzbek government support for his rebellion surfaced, an allegation Uzbek officials denied. Rakhmonov accused former Prime Minister Abdulmalik Abdullojonov of leading the rebellion on 9 November 1998.
His troops killed 10 Tajik government soldiers in Chkalovsk, Tajikistan on 4 November 1998, successfully taking several administrative buildings in Khujand before taking most of Leninabad Oblast. His troops also tried to take control of the city's airport. He asked that at least 40% of all government jobs for northern Tajiks. President Imomali Rakhmonov met with the Tajik Security Council with Zafar Saidov, the president's spokesman, calling the situation "very serious." A few days later the government regained control of the province. When the International Red Cross surveyed the results of the fighting, they found over 2,000 killed, 500 injured. The government declared November 10 a day of mourning.
The Tajik Supreme Court sentenced two of Khudoiberdiyev's militant followers to death on 27 December 1999 for their involvement in clashes with the government in November 1998. 33 other militants were sentenced to prison terms ranging from 10 to 19 years for terrorism and other related charges. 121 of the estimated 1,000 rebels were arrested. The Tajik government again accused the Uzbek government of protecting Khudoiberdiyev.