American Alternative Fuels Act of 2011

American Alternative Fuels Act of 2011 - Amends the Energy Independence and Security Act of 2007 to repeal the requirement that any federal agency procurement contract for an alternative or synthetic fuel, including those from nonconventional petroleum sources, for any mobility-related use (except research or testing) specify that lifecycle greenhouse gas emissions associated with the fuel must, on an ongoing basis, be less than or equal to such emissions from equivalent conventional fuel produced from conventional petroleum sources.

Amends the Energy Policy Act of 2005 to: (1) require the Secretary of Energy to report to certain congressional committees the reasons for any delayed approval of an application for a loan guarantee for a substitute natural gas, chemical feedstock, or liquid transportation fuel project; and (2) make certain substitute natural gas production facilities eligible for loan guarantees.

Amends the Clean Air Act to require the Administrator of the Environmental Protection Agency (EPA), as an algae-based fuel incentive when calculating the applicable volume of renewable fuel for each calendar year, to consider each gallon of renewable biomass produced from algae to be equal to three gallons of renewable fuel if the algae-based fuel was produced using carbon dioxide captured in a manner that prevented its uncontrolled release into the atmosphere during a separate energy production process.

Authorizes the Secretary of Defense (DOD), the Secretary of the Army, the Secretary of the Navy, the Secretary of the Air Force, the Secretary of Homeland Security (DHS), and the Administrator of the National Aeronautics and Space Administration (NASA) to enter into multiyear procurement contracts for alternative fuels, subject to certain requirements.

Amends the Clean Air Act to direct the permitting authority, when establishing the best available control technology for a major emitting facility that is an electric generating facility located in a region in which demand for electricity has increased significantly due to the volume of electric vehicles, to take into account the extent to which emissions of a pollutant have been reduced as a result of the increased use of such vehicles.