Estimation of the influence of different farming systems on emission of greenhouse gases (methane and nitrous oxide) was the aim of the research. The research was conducted on the basis of a special field experiment established in 1994 in the Experimental Station in Osiny in which different crop production systems are compared, and in a group of 20 organic farms organic farms located in the central part of Poland. For the first object the analysis of nitrous oxide emission and soil organic matter balance was done for 1996-2007, whereas for the second one CH4 and N2O emission and potential of sequestration of CO2 in soil organic matter was done for 2004-2005. Organic farming system was characterized by significantly lower nitrous oxide emission in comparison to other systems. There was no distinct difference in CH4 emission between compared systems. In the organic farms, total CH4 and N2O emission expressed in GWP units amounted to 1623 points and this was 22% less than the average value for the Kuyavian-Pomeranian voivodeship. Balance method showed that organic system has a great potential in sequestration of CO2 in soil organic matter in comparison to integrated and conventional systems. However, measurements of humus content in soil did not confirm that observation.