Challenging greenhouse gas (GHG) emission reduction targets were set in Scotland by the Climate Change (Scotland) Act in June 2009. The national objective is to reduce GHG emissions by 42% by 2020 and 80% by 2050 compared to 1990 levels. The GHG emission reduction targets apply both to the traded and non-traded sectors, thus including the rural land use sector. In North East Scotland, rural land uses cover the majority of the land area, with agriculture and forestry representing about 86% and sporting land about 10% of the total area. The objectives of this study were to provide guidance for the development of a regional GHG inventory to estimate methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) emissions from rural land uses in North East of Scotland, to compare with that of the United Kingdom (UK), and discuss the advantages of regional GHG inventories for rural land uses. The study mainly followed the guidance of the IPCC (Intergovernmental Panel on Climate Change) Revised Guidelines for National Greenhouse Gas Inventories and adapts these to the region level. Data available for North East Scotland allowed an assessment of annual GHG emissions from livestock and grassland, cropland management and sporting land, as well as carbon sequestered by forests, between 1999 and 2010. Estimated GHG emissions of 1420 ktCO2e from livestock, grassland and cropland management obtained in this study for 2009 compare well with estimates for the same region from larger-scale inventories. The methodology described, including the steps undertaken for data collection, the shortcomings found and strategies to overcome these, could be applied to other UK or European regions.