Clear Skies Act of 2003

Clear Skies Act of 2003 - Amends the acid deposition control provisions of the Clean Air Act with respect to emissions limitations and allowances programs for sulfur dioxide, nitrogen oxides, and mercury by: (1) revising the allowance system and associated transfer, tracking, permit, compliance plan, and penalty requirements, including those for auctions; and (2) establishing new emissions limitations and trading programs (including implementation of a separate sulfur dioxide scheme for States in the Western Regional Air Partnership).

Requires the Administrator of the Environmental Protection Agency to: (1) promulgate performance standards (limiting emissions of sulfur dioxide, nitrogen oxides, particulate matter, and mercury) for new boilers, integrated gasification combined cycle plants, and combustion turbines; and (2) conduct a comprehensive research and environmental assessment program to enhance understanding of health and environmental effects of particulate matter and mercury and to demonstrate the efficacy of emission reductions under this Act.

Excludes the following units from consideration as major emitting facilities or major stationary sources (or parts thereof) for purposes of compliance with provisions concerning prevention of significant deterioration of air quality and plan requirements for nonattainment areas: (1) those that are subject to the performance standards of this Act; or (2) those with properly operated and maintained equipment to limit particulate matter emissions or subject to a permit under an applicable implementation plan that provides a specified particulate matter emissions limitation and that use good combustion practices to minimize carbon monoxide emissions.

Requires States to ensure in implementation plans that: (1) in an attainment or unclassifiable area, any emissions increase from the construction or modification of an affected unit will not result in exceeding a national ambient air quality standard; and (2) in a nonattainment area, the emissions increase will not interfere with a program to assure the achievement of such a standard. Provides for designation of transitional areas under implementation plans and states requirements for emissions inventories, the attainment of standards by the end of 2015, and penalties for not meeting the eight-hour ozone or fine particles standard.