In 2023, South Korea estimated its greenhouse gas emissions based on the 2006 IPCC guidelines (GLs) in preparation for the 2024 UNFCCC National Inventory Report. This study compared greenhouse gas emissions in the agricultural sector, focusing on rice cultivation and agricultural soil emissions from 1990 to 2021, using both 1996 and 2006 GLs. The objective was to identify the factors causing differences in emissions between these two GLs. The total emissions for 1990 were 15,139 Gg CO2-eq under the 1996 GL and 17,459 Gg CO2-eq under the 2006 GL. By 2021, total emissions were 11,114 Gg CO2-eq for the 1996 GL and 10,392 Gg CO2-eq for the 2006 GL, with the 1996 GL showing a 6.5% higher figure. Methane emissions from rice cultivation in 1990 were 10,533 Gg CO2-eq for the 1996 GL and 14,073 Gg CO2-eq for the 2006 GL, marking a 33.6% increase under the 2006 GL due to a change in methane"s global warming potential (GWP) from 21 to 28. Nitrous oxide emissions from agricultural soil were accounted for 4,656 Gg CO2-eq in 1996 GL and 3,232 Gg CO2-eq in 2006 GL in 1990, reflecting a 17.9% decrease under the 2006 GL, primarily due to the reduced GWP for nitrous oxide from 310 to 265. The study reveals significant shifts in greenhouse gas emissions in agriculture when moving usingfrom the 1996 to 2006 GLs, driven by changes in GWP for methane and nitrous oxide and variations in nitrogen input methods. These findings highlight the importance of guideline updates in accurately accounting for greenhouse gas emissions in agriculture.