In this study, we review the application of epidemiology and economics to decision-making about freedom from aquatic animal disease, at national and regional level, and recent examples from Europe. Epidemiological data (e.g. pathogen prevalence and distribution) determine the technical feasibility and cost of eradication. The eradication of pathogens which exist in wild populations, or in a latent state, is technically difficult, uncertain and expensive. Notably, the eradication of diseases of molluscs is rarely attempted because host populations (farmed and wild) cannot be completely removed from open water systems. Doubt about the success of eradication translates into uncertain ex-ante cost estimates. Additionally, the benefits of an official disease-free status cannot be estimated with any accuracy. For example, in Europe, official freedom from epizootic ulcerative syndrome and white spot syndrome virus has not been pursued, arguably because the evidence does not exist for the benefits (reduced risk of disease in wild populations) to be estimated and thus weighed against the costs of maintaining disease freedom (e.g. restriction on imports). Economic analysis must assess not only whether the benefits of disease freedom outweigh costs, but whether it is the economically optimal disease control option. Government may also want to compare investment in aquatic animal health with other opportunities. As resources become scarce, governments have sought to share costs of disease control with industry, and thus to ensure equity, the distribution benefits must be known so costs can be borne by those who benefit. The economic principles to support decisions about disease freedom are well established, but their application is constrained by lack of epidemiological data, which may explain the lack of economic analysis in support of aquatic animal management in Europe. The integration of epidemiology and economics in disease control planning will identify research aimed at improving the underpinning evidence base.