<ns3:p><ns3:bold>Background:</ns3:bold> Dengue, chikungunya and Zika are viral infections transmitted by <ns3:italic>Aedes aegypti</ns3:italic> mosquitoes, and present major public health challenges in tropical regions. Traditional vector control methods have been ineffective at halting disease transmission. The World Mosquito Program has developed a novel approach to arbovirus control using <ns3:italic>Ae. aegypti </ns3:italic>stably transfected with the <ns3:italic>Wolbachia</ns3:italic> bacterium, which have significantly reduced ability to transmit dengue, Zika and chikungunya in laboratory experiments. Field releases in eight countries have demonstrated <ns3:italic>Wolbachia</ns3:italic> establishment in local <ns3:italic>Ae. aegypti</ns3:italic> populations.</ns3:p><ns3:p> <ns3:bold>Methods:</ns3:bold> We describe a pragmatic approach to measuring the epidemiological impact of city-wide <ns3:italic>Wolbachia</ns3:italic> deployments in Bello and Medellín, Colombia. First, an interrupted time-series analysis will compare the incidence of dengue, chikungunya and Zika case notifications before and after <ns3:italic>Wolbachia</ns3:italic> releases, across the two municipalities. Second, a prospective case-control study using a test-negative design will be conducted in one quadrant of Medellín. Three of the six contiguous release zones in the case-control area were allocated to receive the first <ns3:italic>Wolbachia</ns3:italic> deployments in the city and three to be treated last, approximating a parallel two-arm trial for the &gt;12-month period during which <ns3:italic>Wolbachia</ns3:italic> exposure remains discordant. Allocation, although non-random, aimed to maximise balance between arms in historical dengue incidence and demographics. Arboviral disease cases and arbovirus-negative controls will be enrolled concurrently from febrile patients presenting to primary care, with case/control status classified retrospectively following laboratory diagnostic testing. Intervention effect is estimated from an aggregate odds ratio comparing <ns3:italic>Wolbachia</ns3:italic>-exposure odds among test-positive cases versus test-negative controls.</ns3:p><ns3:p> <ns3:bold>Discussion:</ns3:bold> The study findings will add to an accumulating body of evidence from global field sites on the efficacy of the <ns3:italic>Wolbachia</ns3:italic> method in reducing arboviral disease incidence, and can inform decisions on wider public health implementation of this intervention in the Americas and beyond.</ns3:p><ns3:p> <ns3:bold>Trial registration: </ns3:bold>ClinicalTrials.gov: <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://clinicaltrials.gov/ct2/show/NCT03631719">NCT03631719</ns3:ext-link>. Registered on 15 August 2018.</ns3:p>