This paper describes the epidemiology of dengue in the city of Yogyakarta‚ Indonesia‚ as a prelude to implementing a cluster-randomized trial of Wolbachia for the biocontrol of arboviral transmission. Surveillance records show that hospitalised patients diagnosed with dengue haemorrhagic fever or dengue shock syndrome consisted predominantly of children/adolescents. The majority (68%) of children aged 1-10 years had antibodies indicating past exposure to dengue. Together these results demonstrate a high rate of dengue transmission in Yogyakarta. A mobility survey indicated that children aged 1-10 years spent most of their daytime hours at home. The findings from these descriptive studies inform the design of clinical trials to measure the impact of novel vector control methods by providing baseline data on disease incidence‚ and identifying subpopulations for recruitment into prospective studies of dengue virus infection and disease.