OBJECTIVES: To estimate the cost of illness and the disease burden, in terms of disability adjusted life years (DALYs), for gastroenteritis in the Netherlands in 1999. METHODS: The study population consisted of a community-based prospective cohort study on gastroenteritis, with a nested case-control study, in cooperation with the Dutch sentinel general practice network. Cases with gastroenteritis identified in the cohorts were requested to submit stool samples, complete a questionnaire on risk factors and complete a medical diary for 4 weeks. In this diary, cases reported daily about symptoms, absence from work or school, use of medication and use of health services, such as GP and hospital services. Health services use and productivity losses were valued according to Dutch guidelines for pharmacoeconomic research. DALYs were calculated using data on number of deaths due to gastroenteritis and age at death from Statistics Netherlands. Disability weights for both mild and severe cases of gastroenteritis were taken from a Dutch national study on the burden of diseases. RESULTS: Of the 4860 participants in the cohort, 1052 case episodes were observed. Of these cases, 774 (74%) participated in the case-control component. Of these, 646 (83%) completed data collection. The overall standardised incidence of gastroenteritis was 283 per 1000 person-years, with an estimated total of 4.5 million cases per year. Total costs per case were €68.80, with productivity losses (€55.50) being the major cost driver. Total cost to society were estimated at €308 million in 1999 (95% CI € 221-393 million). Gastroenteritis was associated with a loss of 67,000 DALYs. CONCLUSIONS: Although costs and disease burden are low for individual cases, gastroenteritis is associated with a high disease burden and considerable costs to society due to a high incidence in the population.