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In recent years, number of web-based distance education systems has rapidly increased as a result of improvements in the Internet. Universities have an important role in this situation. Having substantial infrastructures in point of accessing the Internet, permanent education staff and system design team has made distance education more attractive for universities. Distance education systems have begun to make their education activities by using tools and services such as electronic books, electronic mails and conference calls. With the increasing number of these methods and by developing them consistently, the structure that covers the whole system was named the web-based distance education system (WBDES). Although there are many data and information about these systems, there is no detailed information about the software-preparing process and obtained experiences. In this study, a universal WBDES that can be used by all distance education entities has been designed. This WBDES is compatible with any institution or organisation and suitable for universal SCORM standards. It includes many features and functions such as student account creation, user roles, lessons, examinations, security applications, student affairs, counselling services, internal communication, executive functions and assessment, etc. With designed systems, a software infrastructure that is necessary for a virtual academic institution is provided. The system is currently used in Afyon Kocatepe University. While designing the system, MS SQL Server 2005, ASP.NET and C#.NET programming languages were used for the database, web interfaces and programming, respectively. Studies and experiments in designing the system were explained in detail.