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He stood unsuccessfully as a SNP candidate for the House of Commons in the Glasgow Anniesland constituency in the 1997 General Election before standing in the Glasgow Maryhill constituency in both the 1999 and 2003 Scottish Parliamentary elections.
Wilson was also elected chair of the SNP's Glasgow Regional Association in 2001.
In the aftermath of the 2003 election performance of the SNP he became convinced that a change of direction was needed by the SNP leadership. After discussing this with various SNP members he was persuaded to contest the leadership himself and launched a challenge against the SNP leader, John Swinney.
His campaign focused on the issue of centralising the control of the party away from the branches and activists, and what he argued was the trend of placing the SNP ideologically in the centre ground of politics, away from the party's traditional position on the left-of-centre.
In the leadership contest that ensued at the SNP's 2003 Conference Swinney received 577 votes from those delegates voting to Wilson's 111 to remain leader. However, the following year he resigned after sustained media speculation that he was unsuitable for the role. The immediate catalyst for Swinney's resignation was the SNP's poor performance in the elections to the European ParliamentThe European Parliament is the parliamentary body of the European Union. Other organisations of European countries such as NATO, the OSCE, the Council of Europe, and the Western European Union have parliamentary assemblies as well, but the European Parlia, although many spectators commented that Wilson's challenge also contributed to his resignation.
Shortly after the leadership contest he stood down as convenor of the SNP Glasgow Regional Association and was replaced in that position by his leadership campaign manager.