Resources for research, surveillance, control and others public health activities are limited and it is difficult to compare the importance of diseases, which vary in terms of occurrence, impacts, etc. So, in this context of scarce resources and multiple competing priorities, it is necessary to allocate rationally human and financial resources on relevant health priorities. Prioritization is an objective tool to make the best use of limited human and financial resources for funders of research and for organizations in charge of diseases' surveillance and implementation of disease control. In order to develop an efficient method for prioritization of zoonotic diseases in South East Asia, we performed a literature review on the different methods already developed to rank diseases. Several priority setting procedures have been used and described by various organizations (national, regional or international) and technical institutions with different models and goals. Mainly, qualitative and semi-quantitative approaches are used, in which experts are asked to score some criteria against which diseases are prioritized. Few initiatives for quantitative models have been undergone yet, mainly in the field of the food-borne diseases. Whatever the approach used to perform the prioritization exercise, some limitations to the current developed models arise from the analysis of scientific articles and organization reports. Following the identification of weak points in the methods already applied, we discuss about the potential means that can be used to improve current models or to develop innovative tools for prioritization of zoonoses in the specific context of South East Asia.