The rationale for establishing trade 'regions' and 'zones' is based on principles of epidemiological science and risk analysis that assess and manage animal disease risks so that the safety of trade can be ensured. However, the boundaries of geographical regions and zones may readily be breached through numerous epidemiological pathways. The concept of a 'compartment' extends the application of a 'risk boundary' beyond that of a geographical interface and considers all epidemiological factors that can contribute to the creation of an effective boundary. The fundamental requirement for application of either concept (regions/zones or compartments) is that the population considered for trade is maintained within management or geographical boundaries which allow clear epidemiological differentiation to be made between those animals and surrounding populations of higher risk. Seven factors are presented that an exporting country might use to guide the identification and documentation of a compartment. Additionally, the steps that would be undertaken to implement trade based on the compartmentalisation concept are discussed.