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Introduction: Clerkship in field is one of the important educational programs in the field of laboratory sciences and providing opportunities for students to learn in clerkship, improved the quality of health services. The aim of this study was to design a structured microbiology clerkship program from the perspective of case based discussion method among laboratory science students. Methods: This was a single-group intervention study. The participants were from the field of laboratory sciences who participated in clerkship courses (99 participats). Educational intervention based on case-based discussion was designed as a formative evaluation method. Learners' performance was evaluated using a checklist in the stationary test and the students’ satisfaction was evaluated using a questionnaire. The data were analyzed using descriptive and inferential tests. Results: The students' learning scores after the intervention were in desirable level. The highest learning score related to blood culture evaluation was 8.04±1.54 and the lowest score related to wound culture evaluation was 6.26±1.78. There was no significant difference between the satisfaction scores of the course and the performance evaluation scores of students according to academic year. But the performance of senior year students was significantly better and the students’ satisfaction scores were significantly high and at a good level. Conclusion: Using the discussion-based teaching method in the clerkship course increased the students' learning and this method can be effective in increasing the skills and learning of the trainees in the field. It is suggested the case based discussion was used in the instructional design of clerkship courses.