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The objective of this study is to discuss the problems to be come across in new generation web based educational system designs and the solutions derived for these problems. Some of the objects of “challenges” in education applications are formation of domain models belonging to the applications, determination of user knowledge states and formation of adaptive content, link and navigation maps. The problems to be faced in new generation educational systems can be solved by combining adaptive and intelligent approaches adopted in hypermedia models. It is expected that this study might be a guide for developing new generation web-based educational applications.