21st Century Energy Independence Act of 2006

21st Century Energy Independence Act of 2006 - Instructs the Secretary of Energy to seek to ensure: (1) the availability of 200% of the volume of renewable fuels required to be available in the United States by 2013 under the Energy Policy Act of 2005; and (2) the reduction of carbon dioxide emissions from the production and use of renewable fuels by 25%.

Directs the Secretary to establish a loan guarantee program for up to 80% of the cost of a project for: (1) the harvesting, storing, and delivery of agriculture residues for use in cellulosic or traditional ethanol production plants; (2) cellulosic ethanol production technologies that will reduce the initial capital cost to $2.50 per annual gallon, and operation and maintenance costs to 125% of those at traditional corn ethanol plants; (3) advanced biomass gasifiers that can provide specified thermal input requirements for traditional ethanol plants to produce syngas; and (4) scaled catalytic conversion projects to convert syngas to liquid fuels.

Permits such loan guarantees for: (1) a traditional ethanol plant only if the agriculture residue products are used as feedstock to replace thermal input requirements otherwise provided by fossil fuels; and (2) an existing ethanol plant only if the applicant demonstrates the potential to reduce carbon dioxide emissions related to ethanol production by at least 75%.

Authorizes the Secretary to provide grants for up to 50% of the capital costs of the initial commercialization for certain cellulosic ethanol production technologies.