Lewis and Clark National Historic Trail Extension Act of 2006 - Amends the National Trails System Act to extend the Lewis and Clark National Historic Trail to include: (1) the route followed by Meriwether Lewis and William Clark in the preparation phase of their expedition, starting at Monticello, near Charlottesville, Virginia, and traveling to Wood River, Illinois, and in the return phase from Saint Louis, Missouri, to Washington, D.C.; and (2) designated Lewis and Clark sites in Virginia, Washington, D.C., Maryland, Delaware, Pennsylvania, West Virginia, Ohio, Kentucky, Tennessee, Indiana, and Illinois. Directs the Secretary of the Interior to complete a suitability and feasibility study to include the extended route within one year from the date funds are first made available for that purpose.