The implementation of an institutional repository (IR) has never been an easy task since there are challenges that need to be addressed in the pre-implementation process. There are various factors that can interfere with the smooth development of the IR. Awareness, budgeting, technology and human factors such as staffing and depositor’s behaviour all become part of the challenges. Even with thorough planning, there is no guarantee that the IR will work smoothly as there are various post-implementation issues awaiting. As a result, institutions must provide solution plans to encounter all these challenges. This article is a result of a brief comparative study on the challenges and issues experienced by the National University of Malaysia (UKM) and the University of Liverpool in the establishment of IR. The discussions are centered on issues such as depositor’s behavior, management, access and sustainability.