In 2006 the largest of those right-wing groups - the United Self Defence Forces of Colombia - was officially demobilised and disbanded after striking a deal with the government.
But now there are concerns that remnants of these groups have joined forces, fuelled by a surge in drug trafficking, and are presenting a new threat.
Al Jazeera's Teresa Bo reports form the Choco region of Colombia.
See also Sydney Irresistible and Mike Hitchen Unleashed
Putting principles before profits
Putting principles before profits