Climate MATTERS Act of 2008

Climate Market, Auction, Trust & Trade Emissions Reduction System Act of 2008, or the Climate MATTERS Act of 2008 - Declares the purpose of this Act to establish a federal program to reduce US greenhouse gas (GHG) emissions substantially enough by 2050 to avert the catastrophic impacts of global climate change.

Directs the Secretary of the Treasury to establish an international reserve GHG emission allowance program, whose allowance sales proceeds shall be used to mitigate the negative impacts of global climate change on disadvantaged communities in World Trade Organization (WTO) participant countries.

Establishes the International Climate Change Commission to determine annually whether a WTO participant country has taken certain action to limit its GHG emissions.

Amends the Internal Revenue Code to: (1) establish a system for issuing, auctioning, recording, and tracking GHG emission allowances; and (2) impose an excess emissions penalty on owners or operators of covered facilities that fail to submit one or more emission allowances to the Secretary for any year.

Establishes a Carbon Market Efficiency Board to: (1) analyze information on the GHG emission allowance market; and (2) authorize the Secretary to carry out cost relief measures if the market poses a substantial harm to the U.S. economy.

Provides for the distribution of emission allowances to owners and operators of fossil fuel-fired electric power generating facilities and of energy intensive manufacturing facilities.

Establishes: (1) the Deficit Reduction Trust Fund; and (2) the Citizen Protection Trust Fund (CPTF).

Directs the Secretary to administer a Climate Change Rebate Program.

Provides for a healthy families fund.

Sets forth allocations of specified CPTF account funds for: (1) investment in natural resource adaptation to impacts of climate change and ocean acidification; (2) owners and operators of covered facilities who take actions that result in verified GHG emission reductions; (3) states that comply with certain federal building energy standards; (4) states with GHG emission reduction programs exceeding federal GHG emission reduction targets; (5) reductions in GHG emissions from the agriculture and forestry sectors, including those from deforestation activities in foreign countries; and (6) states and load-serving entities that implement energy-efficiency programs.

Requires distribution of certain funds for grants for fixed guideway transit and other specified alternative transportation projects.

Requires the Administrator of the Environmental Protection Agency (EPA) to: (1) develop a federal greenhouse gas registry; (2) make certain GHG emission determinations for covered facilities; and (3) promulgate regulations that require that U.S. GHG emissions in uncovered sectors do not grow.