Emerging and re-emerging zoonotic diseases pose a threat to both humans and animals. This common threat is an opportunity for human and animal health agencies to coordinate across sectors in a more effective response to zoonotic diseases. An initial step in the collaborative process is identification of diseases or pathogens of greatest concern so that limited financial and personnel resources can be effectively focused. Unfortunately, in many countries where zoonotic diseases pose the greatest risk, surveillance information that clearly defines burden of disease is not available. We have created a semi-quantitative tool for prioritizing zoonoses in the absence of comprehensive prevalence data. Our tool requires that human and animal health agency representatives jointly identify criteria (e.g., pandemic potential, human morbidity or mortality, economic impact) that are locally appropriate for defining a disease as being of concern. The outcome of this process is a ranked disease list that both human and animal sectors can support for collaborative surveillance, laboratory capacity enhancement, or other identified activities. The tool is described in a five-step process and its utility is demonstrated for the reader.