The present work aims at studying the local to regional atmospheric pollution transport and transformation processes over the Balkan Peninsula and Bulgaria. The US EPA models-3 system is chosen as a modelling tool. As the NCEP global analysis data with one degree resolution is used as meteorological background, the models nesting capabilities are applied for downscaling the simulations to a 9 km resolution over Balkans and 3 km over Bulgaria. The TNO emission inventory is used as emission input. Special pre-processing procedures are created for introducing temporal profiles and speciation of the emissions. The study is based on a large number of numerical simulations carried out for two emission scenarios – with all the emissions and with biogenic emissions excluded. Some results from both emission scenarios which make it possible to evaluate the contribution of biogenic emissions are demonstrated in the paper.