He was Labour lead on the Scottish Parliament's Enterprise and Lifelong Learning Committee and also a member of the European Committee prior to becoming Deputy Minister for Tourism, Culture and Sport in October 2000 and then Deputy Minister for Environment and Rural Development in November 2001 in the Scottish Executive.

In 2006, Wilson was criticised for remarks he made using the term "attempted rape" to describe talks between the SNP and Scottish Greens.

[1] In the 2007 Scottish Parliament Election he lost his seat Cunninghame North to the Scottish National Party's Kenny Gibson, by only 48 votes in an election with over a thousand spoilt ballot papers, making it the most marginal seat in the country.

Wilson originally wished to challenge the result via a recount but the Scottish Labour Party, following advice from their solicitors, did not proceed with an election petition on his behalf.

[2] In 2008, Wilson was characterised as a whinger by SNP MSP Kenneth Gibson for comments he made about the 2007 count and the presiding officer, who he had called "a clown.