Objective To explore the short term and long term effectiveness of the problem-based learning (PBL) in clinical skill training. Methods A total of 162 clinical medicine undergraduates in Grade 2003 (7-years study) and 2004 (5-year study) who were supposed to intern in the internal medicine departments were randomly divided into the PBL group (n=75) and the control group with traditional training (n=87) for having their clinical skills training. Then t test was applied to compare the two groups about the scores of intern rotation examination and graduate OSCE as well. Results About the baseline: the students in the two groups got similar scores in their internal medicine exam before clinical intern rotation (84.04±7.40 vs. 82.63±8.77, P=0.287). About the short term effectiveness: compared to the control group, the students in the PBL group got higher subjective evaluation from their supervised clinicians (P=0.006). In writing examination, the students of those two group got similar scores in knowledge part (54.17±9.26 vs. 51.67±9.56, P=0.92), while the PBL group won in case reasoning question (20.39±5.27 vs. 16.51±4.90, Plt;0.001). About the long term effectiveness: in the graduate OSCE, the two groups got similar scores in skills operation such as punctures and lab results analyses (P=0.567 and P=0.741), while the students in the PBL group had better performance at the case reasoning and standard patients treating (75.59±9.85 vs. 71.11±12.01, P=0.027). Conclusion With the great short term and long term effectiveness, the PBL applied in the clinical skill training improves the students’ ability of both synthesized analyses and the integrated clinical skills such as clinical thinking and interpersonal communication, but doesn’t aim at the basic knowledge and operation skills.