The purpose of this study was to investigate the outcomes of doctors who studied at a graduate degree program at a domestic institute for clinical medicine.The academic results of 45 doctors who studied at the Graduate Institute of Clinical Medical Sciences-Kaohsiung Branch (GICMS-KB) of Chang Gung University (CGU) were analyzed and compared with those of 83 doctors who had studied abroad or at domestic institutions other than CGU (non-CGU), as well as with 263 who did not pursue further graduate studies (no GS) during the study period from 2003 to 2007. The 128 doctors who had pursued graduate study were sent a survey consisting of 6 questions about factors which hamper research activity.The average number of Science Citation Index (SCI) articles published by the doctors of GICMS-KB as the first author over five years was 3.16 ± 0.52, which was significantly higher than 1.51 ± 0.22 in the no GS group (p = 0.005) and 2.31 ± 0.39 in the non-CGU group. The average number of research grants was 3.62 ± 0.64 in GICMS-KB group, which was higher than 1.57 ± 0.28 in the non-CGU and 1.56 ± 0.20 in the no GS groups (p < 0.001 in both). The percentage of the doctors with faculty positions was 58% in GICMS-KB group, higher than 43% in the non-CGU and 38% in the no GS groups, with a p value of 0.055 comparing GICMS-KB with the no GS group. The survey indicated that all doctors who pursued post-graduate training had similar problems, such as lack of time and lack of research manpower with no difference between the GICMS-KB and non-CGU groups.The academic performance of doctors who did postgraduate study at our graduate institute for clinical medicine was generally better than those who did not pursue further graduate studies or those with postgraduate studies outside CGU. Factors such as adaptation of the GICMS-KB doctors to our system and policies which include enforced grant writing and publication for graduation during the training course may account for the difference.