Introduction: The homepage is the initial place at which the users are directed towards having access to the available resources. This makes web designing of high importance to university administrators and authorities. The purpose of this study was to conduct a qualitative evaluation of websites with WEBQEM in libraries of Medical Universities in the Islamic Republic of Iran. Methods: This study was a descriptive survey which was conducted on 24 websites. Data were gathered on the basis of WEBQEM checklists. Data analysis was performed by using SPSS software version 13. The evaluation was carried out by applying four criteria of WEBQEM. 

Results: The websites' reliability was evaluated as "Very Good", with the average score of 0.82, and its efficiency as "Good" with the average score of 0.64. Usability and functionality scored an average of 0.5 and 0.52, respectively. Finally, half of the websites, on which this study was conducted, were evaluated as "Good "while the other half were as "Average".

 Discussion: Considering the average scores obtained by using the four main criteria of the study, it was conceived that the in terms of functionality and usability of these web sites had some shortcomings. Although reliability and efficiency scored average, some of the websites were not of the expected quality by the main criteria.