A procedure for the assessment of emissions of nitrogen (N) species (ammonia, nitrous oxide, nitric oxide, di-nitrogen) from the manure management system is developed, which treats N pools and flows including emissions strictly according to conservation of mass criteria. As all relevant flows in the husbandry of mammals are depicted, the methodology is considered a Tier 3 approach in IPCC terminology or a detailed methodology in UN ECE terminology. The importance of accounting for all N species is illustrated by comparing emission estimates obtained using this approach with those obtained from the application the present detailed/Tier 2 methodology.