Robust disease burden estimates are important for decision-making concerning introduction of new vaccines. Dengue is a major public health problem in the tropics but robust disease burden estimates are lacking. We conducted a two-sample, capture-recapture study in the largest province in Cambodia to determine disease under-recognition to the National Dengue Surveillance System (NDSS). During 2006–2008, community-based active surveillance for acute febrile illness was conducted in 0- to 19-year-olds in rural and urban areas combined with testing for dengue virus infection. Of 14354 individuals under active surveillance (22498 person-seasons), the annual incidence ranged from 13.4 to 57.8/1000 person-seasons. During the same period, NDSS incidence rates ranged from 1.1/1000 to 5.7/1000, which was 3.9- to 29.0-fold lower than found in the capture-recapture study. In hospitalized cases, the rate of under-recognition was 1.1- to 2.4-fold. This study shows the substantial degree of under-recognition/reporting of dengue and that reported hospitalized cases are not a good surrogate for estimating dengue disease burden.