Background Disease incidence data are needed to guide decision-making for public health interventions. Although dengue is a reportable disease in Thailand and Cambodia, the degree that reported incidence underrecognizes true disease burden is unknown. We utilized dengue incidence calculated from laboratory-confirmed outpatient and inpatient cases in prospective cohort studies to estimate the magnitude of dengue underrecognition and to establish more accurate disease burden estimates for these countries. Methods and Findings Cohort studies were conducted among children aged <15 years by members of a dengue field site consortium over at least 2 dengue seasons. Age-group specific multiplication factors (MFs) were computed by comparing data from three cohort studies to national surveillance data in the same province and year. In Thailand, 14,627 person-years of prospective cohort data were obtained in two provinces and 14,493 person-years from one province in Cambodia. Average annual incidence of laboratory-confirmed dengue was 23/1,000 and 25/1,000 in Thailand, and 41/1,000 in Cambodia. Calculated MFs in these provinces varied by age-group and year (range 0.4–29). Average age-group specific MFs were then applied to country-level reporting data and indicated that in Thailand a median 229,886 (range 210,612–331,236) dengue cases occurred annually during 2003–2007 and a median 111,178 (range 80,452–357,135) cases occurred in Cambodia in children <15 years of age. Average underrecognition of total and inpatient dengue cases was 8.7 and 2.6-fold in Thailand, and 9.1 and 1.4-fold in Cambodia, respectively. During the high-incidence year 2007, >95,000 children in Thailand and >58,000 children in Cambodia were estimated to be hospitalized due to dengue. Conclusion Calculating MFs by comparing prospective cohort study data to locally-reported national surveillance data is one approach to more accurately assess disease burden. These data indicate that although dengue is regularly reported in many countries, national surveillance data significantly underrecognize the true burden of disease.