In order to serve the Islamic researchers, providing a web site is inevitable for Islamic Universities which are in transition from the real to the virtual world and. Today, almost all the major universities in Islamic community have websites. But, in the realization of their mission, it is not clear to what extant these universities were successful in terms of information dissemination. The aim of this paper was to determine the core web sites and evaluate the effectiveness, ranking and collaboration rate among these websites. The formulas of core website determination, co-links and in-links analysis and revised web impact factor were used beside cluster and multidimensional analysis methods in this study. Results showed that "King Saud University" website in Saudi Arabia had the highest visibility and the most authoritative website among all university websites. Also, co-link analysis showed that major Islamic university websites had collaboration in 12 clusters based on clustering analysis and in 11 clusters based on multidimensional analysis, where two of them (Iran and Turkey) were national clusters in cluster analysis method. Results analysis indicated that web designers in these universities must identify how to attract links and web traffic in order to promote the quality and content of websites. However, the ultimate success of a website was dependent upon factors such as quality, size, language, and the approximate age of a website which was not limited to one or two factors.