In this study, an inverse modeling technique is applied to obtain, at a regional scale, top-down emission estimates for nitrogen oxides utilizing tropospheric nitrogen dioxide (NO2) columns retrieved by the OMI/Aura instrument and estimated by the Comprehensive Air Quality Model with extensions (CAMx). The main idea, applied previously using models with coarse spatial resolution, is to combine the a priori information from the bottom up emission inventory used in an air quality simulation that covers the Balkan peninsula in a high resolution grid (0.1° × 0.1°) with the tropospheric NO2 quantities estimated for one complete year by CAMx and the tropospheric NO2 columns retrieved by satellite observations in order to identify missing emissions sources on a regional scale. The results have identified biases between the a priori and a posteriori emission inventories due to the missing emission sources or over-estimation of the spread and quantity of certain emission sources. In such a fine resolution grid we have also analyzed and considered the horizontal transport on the a posteriori NOx emissions. The deduced a posteriori NOx emissions, dominated by the fossil fuel emissions, were found to be1.11 ± 0.30 Tg N/y, compared to 0.87 ± 0.43 Tg N/y found in the a priori Balkan emission inventory. Soil emissions over the extended Greek domain, omitted in the a priori inventory, were estimated to account for almost 20% of the total emitted amount, while for the year 2009 the biomass burning NOx emission flux was also estimated and the average rate accounted for 0.5 × 10−6 Tg N/km2. 2014 Elsevier Ltd.