If the correct structure of Web site is known, the information provider can discover users# behavior patterns and characteristics for better services, and users can find useful information easily and exactly. There may be some difficulties, however, to extract the exact structure of Web site because documents one the Web tend to be changed frequently. This paper proposes new method for extracting such Web structure automatically. The method consists of two phases. The first phase extracts the hyperlinks among Web documents, and then constructs a directed graph to represent the structure of Web site. It has limitations, however, to discover the hyperlinks in Flash and Java Applet. The second phase is to find such hidden hyperlinks by using Web access log. It fist extracts the click streams from the access log, and then extract the hidden hyperlinks by comparing with the directed graph. Several experiments have been conducted to evaluate the proposed method.