Mr Brown also announced plans to offer low-cost loans for existing homeowners to install energy efficient equipment.
Under the plans, new homes will have to be super-insulated to prevent heat loss, and use modern "green" technology to produce their own heat and electricity.
Options include so-called biomass boilers using wood pellets rather than oil or gas, and energy sources such as solar power, pumps extracting heat from the ground, and roof-mounted wind turbines.
Other possibilities include heat exchangers to stop heat escaping with stale air through ventilation systems, and water recycling equipment. Careful design, such as using large south-facing windows to harvest "passive" solar heat, will also be included in the new homes of the future.
New homes will still be able to use electricity from the national grid, but will have to show that they can generate enough surplus power at night to offset any electricity used from the mains. Mr Brown also published plans to waive income tax on any money "green" homeowners make by selling their surplus electricity to the national grid.
Simon Reddy, of Greenpeace, said his organisation was working to build 200 zero-carbon homes in east London. He said Mr Brown’s announcement was "very welcome", but added: "The stamp duty concession is an empty gesture unless the Government makes sure that they build the things."
And the Home Builders’ Federation said builders "want to help people cut their carbon emissions," but urged Mr Brown not to withdraw his stamp duty concession too soon.