Generic frameworks for the economic analysis of farm animal disease are now well established. The paper, therefore, uses bovine viral diarrhoea (BVD) as an example to explore how these frameworks need to be adapted to fit the characteristics of a particular disease and the specific objectives of the analysis. In the case of BVD the relative strength of tests available to correctly identify and then cull the virus positive animals has placed considerable emphasis on cost-benefit analysis of regional and national certification/eradication schemes. Such schemes in turn raise interesting questions about farmer uptake and maintenance of certification schemes, their equity and cost-effective implementation. The complex epidemiology of BVDV infections and the long-term, widespread and often occult nature of BVD effects make economic analysis of the disease and its control particularly challenging. However, this has resulted in a wider whole-farm perspective that captures the influence of decision making beyond those directly associated with disease prevention and control. There has been the need to include management of reproduction, risk and enterprise mix in the research on farmer decision making, which in turn impinge on and are affected by BVD.