Khan supported General Pervez Musharraf's military coup in 1999, believing Musharraf would "end corruption, clear out the political mafias". According to Khan, he was Musharraf's choice for prime minister in 2002 but turned down the offer. Khan participated in the October 2002 Pakistani general election that took place across 272 constituencies and was prepared to form a coalition if his party did not get a majority of the vote. He was elected from Mianwali. In the 2002 referendum, Khan supported military dictator General Musharraf, while all mainstream democratic parties declared that referendum as unconstitutional. He has also served as a part of the Standing Committees on Kashmir and Public Accounts. On 6 May 2005, Khan was mentioned in "The New Yorker" as being the "most directly responsible" for drawing attention in the Muslim world to the "Newsweek" story about the alleged desecration of the Qur'an in a US military prison at the Guantánamo Bay Naval Base in Cuba. In June 2007, Khan faced political opponents in and outside the parliament.