Speaking exclusively to Healthcare Republic, the 66-year-old said he felt he had reached an age where he wanted to spend more time travelling, free of ministerial responsibility.
He plans to visit both Cuba and Mexico this winter.
‘After a busy and enjoyable three-and-a-half years as a DoH minister I have decided to stand down from the government.
‘It is entirely my decision and I will continue to strongly support the NHS reform agenda in the House of Lords and elsewhere.’
Lord Warner took over as minister responsible for GPs and NHS delivery after the May 2005 election.
A series of controversial decisions have made Lord Warner increasingly unpopular with GPs.
Last month he said that practices that did not take part in a controversial accreditation scheme could expect ‘vigorous’ action from their PCT.
Earlier this month GPC threatened to mount a legal challenge to Lord Warner’s plan to cap GP pensions.
Lord Warner told Healthcare Republic he was confident his capping decision was legally sound and would miss day-to-day contact with GPs.
He refused to speculate about the identity of his successor.
Prime minister Tony Blair is expected to announce Lord Warner’s replacement early in 2007.
It is thought likely that Lord Warner’s successor will be new to the government’s health team, possibly from the House of Lords.
It could also trigger a change in the portfolios of the ministerial team at the DoH. This would mean that one of the current team would take over responsibility for GPs.
A BMA spokesman said: ‘We wish him a very good retirement and we look forward to working with his successor.’