Cost-benefit analysis can be used to provide guidance for emerging policy priorities in reducing nitrogen (N) pollution. This paper provides a critical and comprehensive assessment of costs and benefits of the various flows of N on human health, ecosystems and climate stability in order to identify major options for mitigation. The social cost of impacts of N in the EU27 in 2008 was estimated between €75–485 billion per year. A cost share of around 60% is related to emissions to air. The share of total impacts on human health is about 45% and may reflect the higher willingness to pay for human health than for ecosystems or climate stability. Air pollution by nitrogen also generates social benefits for climate by present cooling effects of N containing aerosol and C-sequestration driven by N deposition, amounting to an estimated net benefit of about €5 billion/yr. The economic benefit of N in primary agricultural production ranges between €20–80 billion/yr and is lower than the annual cost of pollution by agricultural N which is in the range of €35–230 billion/yr. Internalizing these environmental costs would lower the optimum annual N-fertilization rate in Northwestern Europe by about 50 kg/ha. Acknowledging the large uncertainties and conceptual issues of our cost-benefit estimates, the results support the priority for further reduction of NH3 and NOx emissions from transport and agriculture beyond commitments recently agreed in revision of the Gothenburg Protocol.