The environmental impact of wheat production was assessed through Life Cycle Assessment (LCA). Local data were collected to characterize Walloon conventional and organic wheat production systems. Two functional units (FU) were investigated: 1 kg of wheat grains at 15% humidity and 1 ha used for wheat cropping. An uncertainty analysis assessed the significance of differences between conventional and organic systems. Using 1 kg of grains as FU, results are not significantly different in global warming and cumulative energy demand. Very highly significant differences for soil acidification and eutrophication, and significant differences for agricultural land occupation were found to be in favor of conventional wheat production. Due to the high yield level in conventional farming (8.5 t/ha at 15% humidity against 4.5 t/ha for organic wheat), organic winter wheat has an equivalent or even, in some impact categories, a higher impact than conventional winter wheat. Using 1 ha as FU, organic production is less impacting than conventional production, except for soil acidification and eutrophication. The choice of the FU has proven to be very sensitive. This study could be improved by accounting for rotation effects, by using more specific models to calculate emissions due to organic and mineral fertilization, and by accounting for carbon storage in soil.