In April 1999, Gibbons was selected as the Labour party candidate for the Aberavon constituency in the new National Assembly for Wales.[3] He was elected in the first Welsh Assembly elections in May, with a majority of 6,743.[4] In October 2000, he was appointed as Deputy Minister for Health by First Minister Rhodri Morgan, providing support to Health Minister Jane Hutt.[5]
He was re-elected in 2003, and appointed as Deputy Minister for Economic Transport and Development shortly after.[6] In August 2003, Gibbons, alongside labour colleague John Griffiths, wrote a submission to the Richard Commission supporting further powers for the Welsh Assembly.[7]
In January 2005, Gibbons was appointed as Minister for Health after prior Health Minister Jane Hutt was removed from the role.[1][8] After being appointed he was given "free rein" over the government's policy on health.[9][10] Gibbons announced he would begin a period of consultation, to determine the best course of action.[10] He faced pressure to adopt similar systems to those used for the English health service, particularly from Wales SecretaryPeter Hain,[11][12][13] and in March 2005 adopted a target for treatment waiting times of no waits longer than six months by 2009.[14]
In the first Cabinet of the Third Assembly he was appointed Minister for the Economy and Transport in May 2007, and Minister for Social Justice and Local Government in the coalition government in July 2007. He then took the decision to stand down at the 2011 Welsh Assembly election and was succeeded by David Rees of the Labour Party.