They purpose of this paper is to explore the difficulties in training physicians after the implementation of the national health insurance system in Taiwan. The data were collected by focus group interview and then analyzed using content analysis. Faculty members from a medical center in southern Taiwan were recruited for this study. The results showed that under the current insurance system there were four areas that have had negative impact on clinical medical education. These include conflict between the managing of hospitals and the training of physicians, insufficient reimbursement to cover the cost of teaching, exploitation of teaching hospitals accreditation system which then affect the quality of clinical teaching, and more emphasis on profits than on medical care. Since the training of physicians is greatly affected by the management of hospitals and the national insurance system, we suggest that the nation's medical insurance policy be integrated and accredited to adopt an appropriate plan for medical training in order to meet the needs of the public. As a reference for future medical education in Taiwan, details of our discoveries, analyses, and a possible solution discussed.