According to the Kenya national climate change action plan, NCCAP (2012), agriculture is the leading source of GHGs, accounting for almost a third of the country’s total emissions. Agricultural emissions are largely generated in the form of methane (CH4) and nitrous oxide (N2O) from crop and livestock production and management activities. Clearing and preparation of land for agricultural production contributes to carbon dioxide (CO2) emission from biomass and soil. The agricultural sector can also play an important role in climate change mitigation, through carbon sequestration in trees on farms and in the soil and potential to reduce agriculture related emissions. The Government of Kenya and other stakeholders are implementing multiple interventions relevant to climate mitigation through agriculture. One notable approach is the climate-smart agriculture through technologies such as conservation agriculture, agroforestry and improved grazing. It is important to quantify the emissions and mitigation potentials of the agricultural sector. This will enable Kenya to provide annual estimates of emissions from all important sources, including farms and capitalize on the emerging green economy. In addition, data on emissions and removals can be used by managers and policy makers to develop strategies for reducing emissions, guide in planning for low-emission development, and monitor the progress of strategies adopted. For example, full development of climate smart agriculture practices and other low carbon actions are expected to almost halve Kenya’s GHG emissions by 2030 (NCCAP 2012). In order to know that with certainty, both baseline emissions and changes will need to be measured and monitored. Collection of data on GHG fluxes is complex and knowledge intensive. It requires knowledge of the underlying mechanisms driving emissions and sequestration as well as the basic scientific techniques to measure. Without a foundation in the practical and theoretical issues, data can be inaccurate because of the substantial impact methods on measurement. This manual aims to bring extension staff up to date with measurement of greenhouse gases in agricultural systems in Kenya, with a focus on direct measurement of actual emissions/removals from sources and sinks within agriculture sector. It provides a snapshot of what greenhouse gases are and how they affect the climate, highlights potential ways of mitigating emissions, and describes measurement methods in easy to read step-wise guidelines.