BackgroundIn 2015, following a call for proposals from the Special Programme for Research and Training in Tropical Diseases (TDR), six scoping reviews on the prevention and control of vector-borne diseases in urban areas were conducted. Those reviews provided a clear picture of the available knowledge and highlighted knowledge gaps, as well as needs and opportunities for future research. Based on the research findings of the scoping reviews, a concept mapping exercise was undertaken to produce a list of priority research needs to be addressed.MethodsMembers of the six research teams responsible for the “VEctor boRne DiseAses Scoping reviews” (VERDAS) consortium’s scoping reviews met for 2 days with decision-makers from Colombia, Brazil, Peru, Pan-American Health Organization, and World Health Organization. A total of 11 researchers and seven decision-makers (from ministries of health, city and regional vector control departments, and vector control programs) completed the concept mapping, answering the question: “In view of the knowledge synthesis and your own expertise, what do we still need to know about vector-borne diseases and other infectious diseases of poverty in urban areas?” Participants rated each statement on two scales from 1 to 5, one relative to ‘priority’ and the other to ‘policy relevance’, and grouped statements into clusters based on their own individual criteria and expertise.ResultsThe final map consisted of 12 clusters. Participants considered those entitled “Equity”, “Technology”, and “Surveillance” to have the highest priority. The cluster considered the most important concerns equity issues, confirming that these issues are rarely addressed in research on vector-borne diseases. On the other hand, the “Population mobility” and “Collaboration” clusters were considered to be the lowest priority but remained identified by participants as research priorities. The average policy relevance scores for each of the 12 clusters were roughly the same as the priority scores for all clusters. Some issues were not addressed during the brain-storming. This is the case for governance and for access and quality of care.ConclusionsBased on this work, and adopting a participatory approach, the concept mapping exercise conducted collaboratively with researchers from these teams and high-level decision-makers identified research themes for which studies should be carried out as a priority.Electronic supplementary materialThe online version of this article (10.1186/s40249-018-0463-y) contains supplementary material, which is available to authorized users.