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Objective: The outbreak of Middle East Respiratory Syndrome (MERS) started in South Korea in May 2015 and the end of crisis was declared in December 2015 by Korea Centers of Disease Control and Prevention (KCDC). However, Zika virus emerged in less than 2 months following MERS and showed higher mortality than other countries. This study is to assess the current prevention system of overseas infectious diseases, based on MERS and Zika virus outbreak and to suggest effective response system for the future. Methods: We conducted two surveys on medical specialists working at tertiary general hospitals regarding the effectiveness of responding system by KCDC against MERS and Zika virus and education in individual medical institutions using 5-Likert points. Response system was examined in three different periods as initial period, spreading period, and post disease period. Results: Although medical specialists received the notifications in initial period, no practical prevention was proven to be placed in responding stage by medical facilities (averagely 3.5/5 points in total and sub-analyses). During spreading period, there were several academic seminars conducted, which were evaluated as helpful. In post disease period, all answered that there were changes on patient treatment in all medical facilities, with mainly report system and the treatment regulations in case of suspicious patients for infection. Only 49% respondents answered positive on the possibility of initial responses. For questionnaire items regarding Zika virus, all answered that there were notifications prior to the first outbreak of the infected patient. Eighty% of respondents were aware of 'the Guideline system for traveling to dangerous areas', and answered that the system was moderately effective (averagely 3.8/5 points in total). For the effectiveness of prevention measures for foreign novel disease by KCDC, the average point was 3.0 in both of total and sub-analyses. Conclusion: There is not enough response system to prevent infectious disease in medical institutional and governmental levels in Korea. It would warrant the modification of overall medical system to improve preventive measures for initial spread of such diseases.