Most soil studies aim a better characterization of the system through indicators. In the present study nematofauna and soil structure were chosen as indicators to be assess soil health as related to agricultural practices. The field research was carried out on the two fodder cropping systems continuous maize (CM, Zea mays L.) and a 3-year rotation of silage-maize – silage-barley (Hordeum vulgare L.) with Italian ryegrass (R3) and grain-maize maintained in these conditions for 18 years. Each crop system was submitted to two management options: 1) the high input level (H), done as a conventional tillage, 2) the low input level (L), where the tillage was replaced by harrowing and the manure was reduced by 30%. The effects of the two different cropping systems was assessed on soil nematofauna and soil physic parameters (structure or aggregate stability). Comparison was made of general composition, trophic structure and biodiversity of the nematofauna collected in both systems. Differences in nematode genera composition and distribution between the two systems were also recorded. The monoculture, compared to the three year rotation, had a negative influence on the nematofauna composition and its ecological succession. The Structural Stability Index (SSI) values indicate that both the cropping systems had a negative effect on the aggregate stability. The results indicate that nematofauna can be used to assess the effects of cropping systems on soil ecosystem, and therefore be considered a good indicator of soil health to integrate information from different chemical or physical indicators.