The purpose of this study was to apply the analytic hierarchy process (AHP) to assist decision-making when planning animal health programmes, by assigning priorities to issues of concern to producers in Chile's main goat production region. This process allows a multi-criteria approach to problems, by analysing and ranking them in a hierarchical structure. Industry experts have highlighted the following animal health and disease control criteria: acceptance by breeders of disease control measures; impact of specific diseases on regional animal trade; the cost and efficacy of control measures; a decrease in flock production; and the impact of caprine diseases on human public health. Using these criteria in the AHP, the study found that the most important impacts were on human public health and on the animal trade. The disease priorities were tuberculosis, brucellosis and echinococcosis/hydatidosis, due mainly to their zoonotic impact. The analytic hierarchy process proved useful when several criteria were involved in public health issues.