Clean Smokestacks Act of 1999 - Amends the Clean Air Act (CAA) to require the Administrator of the Environmental Protection Agency to promulgate regulations to achieve specified reductions in emissions of sulfur dioxide, nitrogen oxides, carbon dioxide, and mercury from powerplants (electric generation facilities with a nameplate capacity of 15 megawatts or greater that use a combustion device to generate electricity for sale) by January 1, 2005.

Requires outdated powerplants, on the later of the date 30 years after the powerplant commenced operation or five years after this Act's enactment, to comply with the most recent new source performance standards under CAA provisions regarding air quality and emissions limitations and with specified requirements for modified sources.

Defines an "outdated powerplant" as a powerplant that has been in operation for 30 years or more.