IPCC Guidelines have been updated after the first official announcement to get more precise estimation of GHG emissions. The goal of this study is to evaluate the implications of the IPCC Guidelines improvements including equations of country-specific parameter values for estimating GHG emissions for rice cultivation on the agricultural sector. In addition, we analyze the effects of emission factors associated with organic amendment applications. The results of this study are as follows; (1) the total GHG emissions of rice cultivation based on 1996 IPCC GL are 28% lower than those estimated by 2006 IPCC GL with the same year data; (2) GHGs can be reduced up to 60% through the assumption of organic fertilizer applications; (3) Jeonnam and Chungnam are the worst regions for GHG emissions on rice cultivation and Chungbuk shows the highest reduction rate of GHG emissions, about 40%.