The interaction between usability and how a Web site is structured is a complicated issue. In this paper, we discuss a Web structure mining algorithm which allows the automatic extraction of navigational structures in a Web site without performing hypertext analysis. We perform several usability experiments to correlate the usability of Web sites and the structural design of the Web site. Experimental results show that the structure mining algorithm gives reasonable prediction about several design issues in Web structure. The analysis serves as building block in the complex issue of web usability and structure mining.