The paper present the results for the influence of investment costs into biogas station on the amount of emissions from the agricultural sector. For the evaluation is applied structural analysis of major factors affecting the level of CO2 emissions from agriculture. Among these factors are: the number of animals (converted to livestock units), cost of investment in biogas plants, the quantity of nitrogen fertilizers and the total amount of CO2 emissions from agriculture. The results show that the investment costs haven ́t significant influence despite the correct direction of effect. Significant impact on CO2 emissions from agriculture have the numbers of animals (respectively cattle units). In the case of applications reviewed model from the Czech Republic to selected countries of the EU shows that the highest investment costs and also decrease CO2 equivalent emissions from agricultural biogas plants is in Germany. The high number of agricultural biogas plants is also evident in Italy and the United Kingdom. Investment costs are in these two countries in the range of 115 to 144 mld. CZK. Furthermore, it is evident that the significant investment costs are incurred by the smaller countries (Czech Republic, Slovakia, Belgium). Investment costs in this case are in the range 10-33 mld. CZK.