A method is presented to quantify the net effect of disease management on greenhouse gas (GHG) emissions per hectare of crop and per tonne of crop produce (grain, animal feed, flour or bioethanol). Calculations were based on experimental and survey data representative of UK wheat production during the period 2004–06. Elite wheat cultivars, with contrasting yields and levels of disease resistance, were compared. Across cultivars, fungicides increased yields by an average of 1·78 t ha−1 and GHG emissions were reduced from 386 to 327 kg CO2 eq. t−1 grain. The amount by which fungicides increased yield – and hence reduced emissions per tonne – was negatively correlated with cultivar resistance to septoria leaf blotch (Mycosphaerella graminicola, anamorph Septoria tritici). GHG emissions of treated cultivars were always less than those of untreated cultivars. Without fungicide use, an additional 0·93 Mt CO2 eq. would be emitted to maintain annual UK grain production at 15 Mt, if the additional land required for wheat production displaced other UK arable crops/set aside. The GHG cost would be much greater if grassland or natural vegetation were displaced. These additional emissions would be reduced substantially if cultivars had more effective septoria leaf blotch resistance. The GHGs associated with UK fungicide use were calculated to be 0·06 Mt CO2 eq. per annum. It was estimated that if it were possible to eliminate diseases completely by increasing disease resistance without any yield penalty and/or developing better fungicides, emissions could theoretically be reduced further to 313 kg CO2eq. t−1 grain.