The Greek electricity generation system is mainly based on the operation of Lignite Thermal Power Stations (LTPSs). In this context, although electricity production from natural gas and renewable forms of energy has increased during recent years in Greece, dominant role of LTPSs is not expected to change dramatically in the near future. As a result, owed to the use of local lignite reserves (poor quality lignite), the Greek LTPSs are responsible for the production of significant flue gas emission quantities. Considering the above, this work is focused on investigating the corresponding long-term NOX and SO2 emissions due to lignite combustion (time period 1995-2008). At this point, it should be noted that although the 5.3GW installed capacity of the lignite-fired power plants represent roughly 40% of the national installed capacity, they are responsible for the noteworthy amounts of 60% and 15% of SO2 and NOX national emissions, respectively. To this end, estimation of SO2 and NOX emission factors is currently undertaken for each Greek LTPS, using available long-term official data. Subsequently, the estimated emission factors are used to classify the Greek LTPSs and evaluate their long-term environmental performance in relation with specific flue gas emissions. According to the results obtained, a clear decreasing rate of flue gases' emissions (especially of NOX) is not the case during the time period analyzed, underlining the necessity for the implementation of effective abatement techniques in the next few years, in compliance with the country's commitments -as an EU Member State-under the corresponding environmental legislation.