Agriculture contributes significantly to the emissions of greenhouse gases in the EU. By using a farm-type, linear-programming based model of the European agricultural supply, we first assess the initial levels of methane and nitrous oxide emissions at the regional level in the EU. For a range of CO2 prices, we assess the potential abatement that can be achieved through an IPCC-based emission tax in EU agriculture, as well as the resulting optimal mix of emission sources in the total abatement. Further, we show that the spatial variability of the abatement actually achieved at a given carbon price is large, indicating that abatement cost heterogeneity is a fundamental feature in the design of a mitigation policy. We assess the efficiency loss associated with uniform standards relative to an emission tax.