Parameters evaluating soil organic matter quantity (organic C and N content) and quality (hot water extractable C content, aliphatic compounds, microbial biomass C content, basal respiration activity) were determined in soils differently fertilized (NPK -mineral fertilization 64.6 kg N/ha/year, FYM -farmyard manure 38.6 kg N/ha/year, FYM + NPK -103.3 kg N/ha/year) in long-term field experiment established in 1955 in Prague. Variant without any fertilization was used as a control. Nine years crop rotation (45% cereals, 33% root crops, 22% fodder crops) is practiced in this long-term experiment. Soil samples were taken from the arable layer (0-20 cm) in spring over the period of 1994-2004. Continual application of FYM and FYM + NPK increased the organic carbon content, hot water extractable C (HWC) content, aliphatic compounds content and microbial biomass C content significantly compared to control variant. Mineral fertilization (NPK) increased only organic C content significantly compared to control variant; HWC content, aliphatic compounds content and microbial biomass C content were increased not significantly. Basal respiration activity did not differ significantly between the variants but the influence of plants cropped in individual years on the basal respiration was observed. The total N content was increased significantly only in FYM + NPK variant as compared to control variant. Presence of lucerne in crop rotation contributed positively to the total nitrogen content in soil of all variants due to the symbiotic N 2 fixation. C:N ratio varied from 9.96 to 10.46. Significant positive relationships (r = 0.30 to 0.68; P < 0.05) among the all parameters were determined with exception of basal respiration activity. The most of measured characteristics tended to be constant or slightly increase in the period of observation that shows evidence of stability of this soil management system.