Production diseases in dairy cows can have significant effects on farm business performance. Decisions about controlling production diseases are mainly based on veterinary advice. However, from an economic perspective, mere diagnosis of disease does not provide enough information for intervention decisions. Well-founded decisions are based on knowledge of the economic effects of production diseases and their control measures. One challenge for dairy farmers and advisors is to access farm-specific tools that can determine the effect of a disease on farm business performance. Efficiency analysis facilitates a more integrated economic-epidemiological view by considering the aggregate transformation of inputs into outputs; it also enables advanced benchmarking within a set of farms. With efficiency analysis, the effect of diseases on economic performance can be studied and farm-specific economic-epidemiological win-win scenarios can be identified. Additionally, the contribution of disease control in moving farms closer to performance benchmarks can be determined. The main challenges for practical application of these techniques are the linking of animal disease metrics with farm accountancy information and integrating farm-economic principles into veterinary advice.