Generally, universities have complex and large websites, which include a collection of many sub-sites related to the different parts of universities (e.g. registration unit, faculties, departments). Managers of academic institutions and educational websites need to know types of usability problems that could be found on their websites. This would shed the light on possible weak aspects on their websites, which need to be improved, in order to reap the advantages of usable educational websites. There is a lack of research which provides detailed information regarding the types of specific usability problems that could be found on universities websites in general, and specifically in Jordan. This research employed the heuristic evaluation method to comprehensively evaluate the usability of three large public university websites in Jordan (Hashemite University, the University of Jordan, and Yarmouk University). The evaluation involves testing all pages related to the selected universities faculties and their corresponding departments. A list of 34 specific types of usability problems, which could be found on a Jordanian university website, was identified. The results provide a description regarding the common types of the problems found on the three Jordanian university sites, together with their numbers and locations on the website.