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Abstract Background The basic science course is the foundation of medical knowledge, and how and in what form the teaching of this course is a vital issue. A successful curriculum should include everything medical students need in their future careers. Basic science education should be such that students clearly understand the relationship between the content and its application in clinical practice. Therefore, the need to change the curriculum of the general medicine course, especially course of the Basic science, in content and layout in an integrated way is felt more than before. This study was designed to explain the experiences of medical students from the Shiraz University of Medical Sciences since the implementation of integration in 2020. Methods The present study was qualitative research with a conventional content analysis method. Participants were selected for the interview purposefully. They included 12 Medical students from basic and clinical sciences and 5 faculty members. Data were collected through semi-structured interviews and the content analysis method. Four methods of Goba and Lincoln were used to evaluate the accuracy of the data. Results After summarizing and analyzing the data, 221 codes were extracted. They were divided into seven subcategories and finally, three main themes including Enjoyable experiences (advantages of the integration system), Upsetting experiences (Disadvantages of the integration system), Resolutions to solving integration problems were extracted. Generally, the findings indicated a positive evaluation of medical students of Shiraz University of Medical Sciences from the integration system, and they stated that the integration causes an interaction between basic and clinical sciences and also increases students’ motivation. Conclusion The findings indicated a positive evaluation of Shiraz’s medical students of the integrated system. According to the results of this research, it can be said; that the use of integration horizontally and vertically in medical education improves the quality of education compared to traditional methods. The integration of basic and clinical science is important in the sense that can be a powerful tool for learning and acquiring skills, also, it can also help in the promotion of professional development of students and motivate them to study more in interactive manner and be loyal to lifelong learning. study generally showed that combining theoretical and practical courses has advantages and disadvantages, but its advantages are more. Paying attention to the shortcomings, especially in the supply of human resources and professors, and reforming the program with continuous revision are issues that education managers and medical educators of the general medical practice should address.