This study intended to explore the principles and process of user-centered design model for developing Problem-Based Learning environment via Web and to identify its areas for improvement on the basis of users\' responses. Periodontal science class in a dental college was chosen as a case and the principle and process of user centered design were analysed according to developmental research methodology. The result of the case study was used to modify the user centered design model which had been developed on the basis of the literature review. The actual process of user centered design was consisted of ten phases: analysis, instructional design, development of prototype, usability test of prototype, modification of prototype, development of program, usability test of program, modification of program, implementation, usability test of implementation. Forty percent of the total developmental period was spent on the development and modification of prototype, and in this period, concurrent design and participation of the users were happened most actively. The students showed a relatively high level of satisfaction with the final product of the web-based problem-based learning and the instructors also responded positively to the process and result of the user centered design. Finally, the areas of improvement to apply more effectively the user centered design are identified: the period and method of usability test, repeated design in the early developmental period, usability test for educational aspects, cost of usability test, efficient communication method, positive user\'s participation.