Alternative Liquid Transportation Fuel Promotion Act of 2006 - Amends the Energy Policy Act of 2005 to declare eligible for a federal loan guarantee commitment large-scale coal-to-liquid facilities that use coal resources of the United States to produce at least 5,000 barrels a day of liquid transportation fuel.
Directs the Secretary of Energy to establish a federal loan program to pay the federal share of the cost of obtaining any services necessary for the planning, permitting, and construction of a coal-to-liquid facility.
Amends the Energy Policy and Conservation Act to direct the Secretary to study and report to certain congressional committees on the feasibility and suitability of maintaining coal-to-liquid products in the Strategic Petroleum Reserve.
Authorizes the Secretary to construct or lease storage facilities in the vicinity of pipeline infrastructure and at least one military base, but outside the boundaries of any state on the coast of the Gulf of Mexico.