Objective Nationwide prevalence studies on malnutrition in hospitalised children have not been done. This study aimed to investigate the prevalence of malnutrition of all newly admitted children in The Netherlands during 3 consecutive days. Design Prospective observational study. Setting Paediatric wards of 44 hospitals (7 academic and 37 general). Participants A total of 424 children aged>30 days and hospitalised for > 1 day were included, 63% male, 86% non-white. Median age was 3.5 years and median hospital stay was 2 days. Main outcome measures SD scores ,22 for weight for height and height for age were considered to indicate acute and chronic malnutrition, respectively. Results Overall 19% of the children had acute and/or chronic malnutrition at admission (academic 22% and general 17%). The proportion of children with chronic malnutrition was significantly higher in academic hospitals (14% vs 6%). Logistic regression analysis allowing for age, underlying disease, ethnicity, surgery and type of centre showed a significant relation between the presence of malnutrition at admission and underlying disease (odds ratio (OR) 2.2). For chronic malnutrition both underlying disease and non-white ethnicity were significantly related to a higher prevalence (OR 3.7 and OR 2.8, respectively). Multiple regression analysis showed that children with acute malnutrition stayed on average 45% longer (95% CI 7% to 95%) in the hospital than children without such malnutrition. Conclusions This unique nationwide study shows that 19% of children admitted to Dutch hospitals are malnourished at admission. This high prevalence underlines the need for routine screening and treatment of malnutrition in hospitalised children.