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This study compares three approaches in the monitoring of ammonia (NH3) emissions from intensive breeding of fattening pigs in relation to compliance with the standards arising from the requirements of Integrated Pollution Prevention and Control (IPPC) used in the Czech Republic. The first approach was based on the determination of NH3 emissions calculation by measurement using reduced sampling days focused on the final fattening phase. The second approach was based on the determination of NH3 emissions calculation by measurement respecting the Best Reference Document for Intensive Rearing of Poultry or Pig (BREF IRPP) and relevant best available techniques (BAT) conclusions under Directive 2010/75/EU. The third approach was based on estimation by using emission factors respecting BREF IRPP and Methodological Instruction of the Air Protection Department of the Czech Republic. The results show that the determined emission factors in the Czech Republic may not always reflect the actual production of NH3 emissions even when reduced by the applied BAT. Determination of NH3 emissions calculation by measurement respecting BREF IRPP represents the predominant phases of fattening (refinement) and microclimatic conditions; however, it is time and money-consuming.