There are many kinds of Chinese traditional patent medicine used in clinical practice and many adverse events have been reported by clinical professionals. Chinese patent medicine's safety problems are the most concerned by patients and physicians. At present, many researchers have studied re-evaluation methods about post marketing Chinese medicine safety inside and outside China. However, it is rare that using data from hospital information system (HIS) to re-evaluating post marketing Chinese traditional patent medicine safety problems. HIS database in real world is a good resource with rich information to research medicine safety. This study planed to analyze HIS data selected from ten top general hospitals in Beijing, formed a large HIS database in real world with a capacity of 1 000 000 cases in total after a series of data cleaning and integrating procedures. This study could be a new project that using information to evaluate traditional Chinese medicine safety based on HIS database. A clear protocol has been completed as for the first step for the whole study. The protocol is as follows. First of all, separate each of the Chinese traditional patent medicines existing in the total HIS database as a single database. Secondly, select some related laboratory tests indexes as the safety evaluating outcomes, such as routine blood, routine urine, feces routine, conventional coagulation, liver function, kidney function and other tests. Thirdly, use the data mining method to analyze those selected safety outcomes which had abnormal change before and after using Chinese patent medicines. Finally, judge the relationship between those abnormal changing and Chinese patent medicine. We hope this method could imply useful information to Chinese medicine researchers interested in safety evaluation of traditional Chinese medicine.