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Purpose-The main goal of this paper is to highlight the lessons learned and good practices regarding the greenhouse inventory system in the Republic of Macedonia. Design/methodology/approach-A comparative analysis for the preparation of the three national communications to UNFCCC in Republic of Macedonia. Findings-The findings reveal the shift from a project-approach, based on external consultants, towards a more process-oriented-approach, where a multidisciplinary national team has been established to prepare the inventory. Also, notable results include improvements in the technical capacity of the inventory team, communications with data sources and other stakeholders, Quality Assurance/ Quality Control procedures, documenting and archiving, regional cooperation, as well as, the reliability of data series for GHG emissions. Practical implications-The study may serve well for countries with similar national circumstances and priorities for preparation of greenhouse inventory systems. Originality/value-Developing national database (inventory) of greenhouse gases is an essential first step toward managing better climate change policy planning. A complete and transparent national greenhouse inventory is an essential tool for understanding emissions and trends, projecting future emissions and identifying sectors for cost-effective emission reduction opportunities. It is also a core element of National climate change reports to the UNFCCC (National Communications). This case study shows the development of a sustainable system for preparation of greenhouse gas inventories and it describes the data collection and analysis procedures within that system.