Clean Trucks Act of 2004 - Amends Federal transportation law to require motor carriers, as part of registering with the Secretary of Transportation to provide transportation, to comply with the heavy duty vehicle and engine emission performance standards and related regulations established by the Environmental Protection Agency (EPA).
Directs the Administrator of the Federal Motor Carrier Safety Administration to: (1) collect annually information on the year, make, model, certification level, travel routes, trip duration, fuel quality and consumption, and related activities of long-haul heavy duty trucks operating in the United States; and (2) submit such information to the Adminstrator of the EPA for use in developing and publishing estimates of the total national emissions of all criteria pollutants and hazardous air pollutants associated with long-haul heavy duty trucks.