Navigability refers to how easy a user can find desired information in a web site and is influenced by the structure of a web site. In this paper, we created three types of Web sites, that is a Web site whose structure forms a small world, a Web site whose structure forms a semi-matroid, and a Web site based on an ontology and measured the navigability of each Web site based on two criteria (the number of hyperlinks clicked by users to find the desired information and the elapsed time for finding the desired information). The reason that we selected three structures is because hyperlinks can be created in a way that helps a user find desired information in each site. From the experiments, we found that the average number of hyperlinks which a user clicked to find out the desired information was as follows: a Web site that had semi-matroid property (100.37 hyperlinks) < a Web site that was created based on an ontology (117.63 hyperlinks) < a Web site that had small-world property (236.17 hyperlinks). In addition, we found that the average elapsed time during which a user found out the desired information was as follows: a Web site that was created based on an ontology (20 min 26 sec) < a Web site that had semi-matroid property (23 min 6 sec) < a Web site that had small-world property (30 min 47 sec). Therefore, we can consider a Web site that is created based on a semi-matroid or an ontology is relatively more navigable than a Web site that has small-world property. In this paper, we also propose a way by which our experimental results can be reflected in designing an educational Web site.