The dramatic expansion of Korean agro-food industry and the increase of agro-food imports make Korean food consumers concerned with agro-food safety. In addition, the recent outbreaks of food-borne diseases, including mad cow disease (BSE) and the High Pathogenic Avian Influenza (HPAI), have exacerbated the jitters about agro-food safety control policy. In order to manage agro-food safety, the Korean government has implemented various agro-food safety management systems. However, the Korean agro-food safety system still has many problems, which are barriers to a safer agro-food environment in Korea. This paper analyzes the current situation of the agro-food safety system in Korea and the issues related with the risk analysis system, and reviews agro-food safety programs and outstanding issues. Then, a new agro-food safety system and polices are proposed as the results of this study.