This research aims to investigate visibility of Iranian journal web sites by examining hyperlinks paying to them in order to determine their impact in national and international level. In this study high ranking journal web sites will be introduced and the sources of links to them will be analyzed. Via webometric study the links to 32 journals were counted and analyzed. The findings showed that Archives of Iranian Medicine web site attracted the highest in-links to its web site. The older journal web sites and web sites with more content attracted more inlink pages. The study also showed that more than 30% of these links are research related links which were made out of research motivations. From the journals impact in national and international view, findings showed that nearly 93% of links came from the journals own country. These information can aware web site designer of the web site position in the scientif