Integrated assessments that analyze global warming, acidification, eutrophication and ozone related problems simultaneously, need complete, detailed and consistent emission estimates that consider possible interrelations between different pollutants. We discuss three types of emission estimation methods: emission factor, regression analyses and process-based methods. Selected examples of these are reviewed to illustrate the large variety in methods available. We present an approach for the evaluation of emission estimation methods which follows three steps: (1) Comparison, (2) Scoring and (3) Multi-Criteria Analysis (MCA). We demonstrate the usefulness of this approach by applying it to a case study for the Czech Republic. Firstly we compare selected methods with respect to characteristics which we consider as requirements to quantify emissions of air, water and soil pollutants in an integrated way. We observe that none of the selected methods fully meet our defined characteristics. Secondly, we score the methods with respect to three types of criteria. This evaluation reveals large differences between the methods. We conclude that the following methods best meet our criteria: the IPCC Guidelines, methods from INITIATOR, and the detailed method of the EMEP/CORINAIR Guidebook. Finally, we perform a Multi-Criteria Analysis to analyze how our conclusions change if one considers certain criteria as more important than others. Based on this analysis we suggest that combining parts of each of the three methods forms a sound basis for a new emission estimation method for quantifying agricultural emissions of air, water and soil pollution simultaneously.