There is significant potential for GHG mitigation in agriculture. Nutrient leakage from farming systems, in terms of greenhouse gases and other environmental pollutants, will attract costs and so, breeding strategies will need to be tailored to optimise production within nutrient use constraints. This study has shown that there is potential to reduce emissions from livestock systems by selection on correlated traits. For example, selecting on traits that improve the efficiency of the system (e.g. residual feed intake, longevity) has a favourable effect on system emissions as well as improving future sustainability of the system. The development of breeding goals that incorporate environmental concerns is both desirable and possible. However, new measurement techniques for direct and indirect emissions will improve the potential to reduce emissions by harnessing these measurements in genetic selection.