In 1999, the costs of gastroenteritis in the Netherlands were estimated using data on hospitalizations from national registries, together with data on etiology and self-reported data on health care resource use in a community-based study. Now, more information on hospitalizations is available and these data were used to update the total costs of gastroenteritis in the Netherlands. The costs of severe gastroenteritis in the Netherlands were estimated in more depth using a hospital-based study, with patient questionnaires including a follow-up period of 6 months. The overall costs of gastroenteritis were calculated taking direct medical costs, direct non-medical costs, and indirect non-medical costs into account. The costs for severe gastroenteritis in 2009 were estimated at €2,203 per hospitalized child and €6,834 per hospitalized adult. The overall costs of gastroenteritis in 2009 were estimated at €611–695 million, which is €133–151 per gastroenteritis case or €37–42 per inhabitant. The total health care costs for gastroenteritis were about 50% higher in 2009 compared to 1999, which is mostly due to the rise in health care costs. The costs per gastroenteritis episode in adults are higher compared to children, mainly due to differences in the reasons for hospitalization and course of disease, and productivity losses.