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This study investigated the university professors', pre-service teachers' and in-service teachers' perceptions of the specialized science education courses in the 11 national universities of education in Korea, analyzed their perception differences, and made suggestions the future directions for the specialized courses. For this study, 46 university professors, 402 in-service teachers, and 336 pre-service teachers were participated nationwide. The results show that there were significant differences in their perceptions between the three groups. For university professors, for example, the acquisition of science content knowledge appeared to be the most important objective of the courses, whereas the other groups preferred the acquisition of more practical knowledge and skills that they could easily use and apply in their classroom teaching later. The university professors tended to think that the science specialized courses would be very useful to the teachers' teaching and contribute to developing their professionality. On the contrary, the in-service and pre-service teachers tended to think that the courses would be not so useful because science theories construct the courses rather than practical knowledge. The implications of these findings are discussed in relation to the future science teacher education.