A method and system for autonomously downloading and indexing Hidden Web pages from Websites includes the steps of selecting a query term and issuing a query to a site-specific search interface containing Hidden Web pages. A results index is then acquired and the Hidden Web pages are downloaded from the results index. A plurality of potential query terms are then identified from the downloaded Hidden Web pages. The efficiency of each potential query term is then estimated and a next query term is selected from the plurality of potential query terms, wherein the next selected query term has the greatest efficiency. The next selected query term is then issued to the site-specific search interface using the next query term. The process is repeated until all or most of the Hidden Web pages are discovered.