ATutor is an open source web-based learning management software which has been designed for institutional e-learning management including content creation, learner’s activity management and tracking learning objectives in a social networking environment, using various online communicative tools. This paper describes how this software is used in a medical university, explaining boundaries and challenges. This is a case-study focusing on preparation of content for students of higher education institutions in Medical Sciences. The focus is on supplementary resources for students and continuous medical education. Despite the initial resistance and challenges of using open source software without technical supports, the process was progressive and lead to development of education. Many conflicts and challenges were resolved in the first year of the study while some features of the software proved to be incapable for medical education learning material and usability rate in some tools was very low. Despite boundaries and difficulties in moving toward electronic learning for medical education, using open source softwares such as Atutor is possible and beneficial. Customizing the software, preparation of IT infrastructure and access to a technical team to develop and manage the virtual environment of e-Learning is essential. Otherwise the system would not widely be accepted by users, this raises problems that lead to strongly negative feedback from tutors and learners.