This paper proposes the evaluation methods for measuring retrieval effectiveness of Web search engine systems, attempting to make them suitable for real Web environment. With this objective, we constructed 100-gigabyte and 10-gigabyte document sets that were mainly gathered from the '.jp' domain, and conducted an evaluation workshop at the third NTCIR Workshop from 2001 to 2002, where we assessed the retrieval effectiveness of a certain number of Web search engine systems using the common data set. Conventional evaluation workshops assessed the relevance of the retrieved documents, which were submitted by the workshop participants, by considering the contents of individual pages. On the other hand, we assessed the relevance of the retrieved pages by considering the relationship between the pages referenced by hyperlinks.