Green Vehicles Promotion Act of 2006 - Amends the Internal Revenue Code to allow tax credits through 2010 for the purchase of a qualified flexible fuel motor vehicle and for the conversion of an existing motor vehicle into a qualified flexible fuel motor vehicle. Defines "qualified flexible fuel vehicle" to include a vehicle using fuel with an 85% ethanol content.
Establishes in the Treasury the Alternative Fueling Infrastructure Trust Fund to create a grant program for the construction and operation of alternative fuel refueling stations. Defines "alternative fuels" to mean: (1) fuels with an 85% ethanol content, liquefied petroleum gas, or hydrogen; or (2) biodiesel mixtures.
Directs the Secretary of Transportation to remit 90% of the civil penalties collected for violations of automobile fuel economy standards to the Trust Fund.