The main model used for the preparation of inventory of greenhouse gases it is evaluation of emissions by using specific emission factors of pollution sources and related activities data (E=kemisxaactiv) [1,2,3]. Nontherless, the simplicity of this modelling the national and international experiences in GHG assessments reveal a series of problems in the field. Thus, emission factors have been depicted in wide ranges both in the EMEP/CORINAIR (the Core Inventory of Air Emissions in Europe) and IPCC (Intergovernmental Panel for Climate Change) methodologies elaborated within UNECE Convention on Long-Range Transboundary Air Pollution and respectively United Nations Framework Climate Change Convention and for their selection and use national features and alternative models & methodologies have not being always taken into account. These circumstances have led to low precision of the data included both into National Environment Reports and international ones (the uncertainties for the values of total annual national emission varies sometimes between 30-50%). While implementing UNDP-GEF Regional Project “Capacity Building for Improving the Quality of GHG Inventories (Europe/CIS region)” the Republic of Moldova’s National Program to Improve the Quality of GHG Inventory is currently under developing, which builds capacity for strengthening institutional framework to prepare on regular basis the GHG inventory and improving the quality of data inputs to national GHG emissions and sinks. The document it is followed by the development of two complimentary documents: “Republic of Moldova Manual of Procedures for National GHG Inventory” which describes the process of preparation the GHG inventory and the “National Quality Assurance/Quality Control and Uncertainty Management Plan” which includes a rigorous set of activities having the scope integration the quality control and the quality assurance procedures at each stage of the estimation and development of the national GHG inventory (the process being ensured by improving verifications at each stage of assessment and inventory development, by involving national GHG experts on on-going basis, by maintaining an open and transparent process of the inventory preparation, using reviewing process and by ensuring a continuing communication among the participants; in the same context, the uncertainty analysis it is treated in the document as an instrument that facilitates the process of maintaining and improving the quality of national GHG inventory).