Abstract Background National public health agencies are required to prioritise infectious diseases for prevention and control. We applied the prioritisation method recommended by the European Centre for Disease Prevention and Control to rank infectious diseases, according to their relative importance for surveillance and public health, to inform future public health action in Belgium. Methods We applied the multi-criteria-decision-analysis approach. A working group of epidemiologists and statisticians from Belgium (n = 6) designed a balanced set of prioritisation criteria. A panel of Belgian experts (n = 80) allocated in an online survey each criteria a weight, according to perceived relative importance. Next, experts (n = 37) scored each disease against each criteria in an online survey, guided by disease-specific factsheets referring the period 2010–2016 in Belgium. The weighted sum of the criteria’s scores composed the final weighted score per disease, on which the ranking was based. Sensitivity analyses quantified the impact of eight alternative analysis scenarios on the top-20 ranked diseases. We identified criteria and diseases associated with data-gaps as those with the highest number of blank answers in the scoring survey. Principle components of the final weighted score were identified. Results Working groups selected 98 diseases and 18 criteria, structured in five criteria groups. The diseases ranked highest were (in order) pertussis, human immunodeficiency virus infection, hepatitis C and hepatitis B. Among the five criteria groups, overall the highest weights were assigned to ‘impact on the patient’, followed by ‘impact on public health’, while different perceptions were identified between clinicians, microbiologists and epidemiologists. Among the 18 individual criteria, ‘spreading potential’ and ‘events requiring public health action’ were assigned the highest weights. Principle components clustered with thematic disease groups. Notable data gaps were found among hospital-related diseases. ...