The performance of two systems of semi-industrial up-flow biological aerated filters (BAF) with pre-denitrification followed by nitrification was studied and compared under various operating and loading conditions. The first system consisted of two separate reactors for the denitrification and the nitrification step, whereas in the second system the aerobic nitrification zone was packed on top of the anoxic denitrification zone in one reactor. The second system potentially offers substantial savings in investment costs and space requirements for a large scale treatment plant. Regarding the elimination of carbonaceous pollution and denitrification the systems did not show significant differences. However, nitrification in the combined system suffered from the mixing of different biocenosis by daily backwashing and was reduced to 50-70% of the separated system's performance. Factors such as oxygen concentration, raw water composition and loading rates affected both systems' nitrification rates in similar ways. Since it is impossible to optimise the nitrification and denitrification processes separately, the combined system should only be considered for large scale applications if space is very scarce and if a stable raw water composition can be expected. If strict limit values for nitrate have to be met in the effluent, a combination of pre- and post-denitrification is advantageous and advisable.