The paper focuses on quantitative assessment of nitrogen flows in a livestock farm under transition to best available techniques BAT system in Russia. Comparative analysis of quantitative estimates of ammonia emissions from housing for dairy cows, fattening pigs, farrowing sows and laying hens was conducted using available literature data and information obtained through a survey of pilot livestock farms in Leningrad Region. Ammonia emission data for existing Russian enterprises were found in the range of BREF emission levels associated with BAT. The nitrogen farm-gate balance was calculated for the farm with 810 dairy cows, 2600 ha of agricultural land and milk yield of 22 kg/day. The nitrogen surplus was 48.3 kg/ha, which was below the limit values and indicated the possibility to increase the application amount of nitrogen fertilisers, however, nitrogen use efficiency of 0.21 was significantly below the European average. The viability of manure storage and spreading techniques recommended by European BREF, namely compost heaps covering and immediate incorporation of organic fertilisers after spreading, was estimated for this farm. The calculated values of total nitrogen losses are reduced by 20%; the saving of mineral fertilizers owing to higher nitrogen content in applied organic fertilisers can be 18 t / year. For the rough assessment of technologies on the initial stage of Russian reference books creation it is practicable to use the data from EU BREF on intensive rearing of pigs and poultry. When farms are assessed on the stage of integrated permits issue, it is feasible to use the measured air concentrations of hazardous substances along with the estimation of the whole-farm environmental impact by nitrogen use efficiency. For such estimates to be applied in Russia, the data needs to be collected and systematised for different categories of farms and for different climatic regions.