Along with increasing interest in organic farming or environmental-friendly, land application of compost for crop production has been increased substantially. However, livestock manure based compost is a composite of myriad microbes of which some might be harmful to human being. Thus appropriate application guidelines need to be developed for safe compost use for agricultural purpose. The objective of this study is to develop a framework for the microbial risk assessment associated with compost farmland application. The procedure of the microbial process involves identification of potential hazardous microbes that may exist in compost, exposure assessment of farmer to pathogenic microbes, and application of dose-response relationship to derive application concentration. The concentrations of potentially pathogenic microorganisms in compost necessary to achieve a 1:10,000 annual risk of infection will be estimated to be proposed as the compost quality to be met for safe use and agricultural production. In this study, rice paddy farming which is the most prevailing practice in Korea was considered as the cultivation type. Typical rice farming practice was set into a scenario of which each process was evaluated in terms of microbial exposure and thus health effects on farmers. The whole assessment process was incorporated into the microbial risk assessment framework for the compost land application. The established framework will provide us a platform for microbial risk assessment in association with compost application for agricultural purposes.