A method and system of creating and customizing multiple roots in a navigation pane are described. By selecting desired pages and adding them to the navigation pane, users may create multiple roots with which to navigate. A multiple roots navigation system permits the user to bypass irrelevant pages while reducing the amount of information presented in the navigation pane. The individual root nodes may further be customized to reflect ownership, importance or general aesthetic preferences. Using multiple roots, a user is not restricted to a single hierarchical display structure.