Disease related malnutrition (DRM) is a serious medical condition which is associated with an increase in morbidity and mortality, augmenting resource use and associated costs. DRM can be detected by actively and fully assessing the nutritional status. Studies in adult malnourished patients have shown that the additional health care costs are about € 2 billion (€ 2000 million) per year. The objective of the current study was to estimate the annual additional costs of DRM for pediatric patients as was done for adults. A cost-of-illness analysis was performed to calculate the annual additional costs of DRM in 2015 pediatric patients (aged 1 month up to and including 17 years) admitted to non-academic hospitals in The Netherlands. DRM was assessed with weight-for-age, weight-for-height and height-for-age. Input variables in the formula used were length of stay and prevalence of DRM. The costs were estimated per disease as classified in the International Classification of Diseases by the WHO (ICD-10), per gender and age group. The results were expressed as an absolute monetary value as well as a percentage of the Dutch national health expenditure. Robustness of the results was checked by a sensitivity analysis. The total additional direct medical costs of DRM in pediatric patients in 2013 were estimated to be € 51 million for acute malnutrition, € 46 million when focused on chronic malnutrition and € 80 million in case of overall malnourished children. This equals 5.6% of the total Dutch hospital costs for these hospitalized children. This study has shown that DRM in hospitalized children is associated with an increase in annual hospital costs with an additional amount of € 80 million, of which acute malnutrition account for the largest part.