The dynamics of greenhouse gases at the soil surface and the role of agroecosystems as their source or sink are not completely understood. This study was conducted to estimate fluxes as emission/uptake rates and variability of carbon dioxide, methane and nitrous oxide in corn cropping systems. In this field study, soil surface fluxes were determined in Drummer and Raub soil series by static-chamber during two growing seasons (March to November of 2005 and 2006) in four corn cropping systems: continuous corn with inorganic nitrogen (CCIN), corn-soybean rotation with inorganic nitrogen (CSIN), continuous corn with either spring (CCSM) or fall manure (CCFM). In addition, soybean (grown in the CSIN) and prairie grass (as natural reference ecosystem) were assessed. The CO₂ fluxes were directly correlated to air temperature (r: 0.55***) as well as N₂O fluxes to air temperature (r: 0.14***) and soil moisture (r: 0.17***). Seasonal CO₂ emissions were not different among corn treatments (6.2 Mg ha^-1), while short term (2 weeks) losses were enhanced after manure applications. No net seasonal fluxes were registered for CH₄ although modest, intermittent temporal uptakes were observed. Seasonal N₂O fluxes were different among treatments (CCIN=CSIN=CCSM: 12.6 > CCFM: 5.3 > PG=SC: 0.5 Kg ha^-1), and they were driven by pulse emissions following the nitrogen applications. Variances of CO₂ and N₂O emissions and sampling intervals were correlated within a range up to 9 and 5 days, respectively. Temporal, between and within year variability appeared to be more strongly affected by changes in local environmental conditions than by agricultural management especially for CO₂, which translates into complexity when scaling these experimental results to a regional landscape.