To protect patients' privacy and to improve the convenience of research, Asan Medical Center (AMC) has been developing a de-identification system for biomedical research, which mainly consists of three components: de-identification tool, search tool, and chart review tool. The de-identification tool can substitute a randomly assigned research ID for a hospital patient ID, remove the identifiers in the structured format, and mask them in the unstructured format, i.e., texts. The search tool can find the number of patients which satisfies given criteria. The chart review tool can provide de-identified patient's clinical data for review. We found that clinical data warehouse was essential for successful implementation of de-identification system, and this system should be tightly linked to an electronic institutional review board system for easy operation of honest brokers.