The objective of this study was to provide data on malnutrition prevalence in hospitals, nursing homes and home-care organisations in The Netherlands in a nationally representative sample, and to assess the factors such as age, sex, time since admission, ward type and disease for identifying patients at high risk of malnutrition. A cross-sectional, multi-centre design with a standardised questionnaire was used to measure the prevalence of malnutrition. Nutritional status was assessed by BMI, undesired weight loss and nutritional intake. In this study, 12 883 patients were included. The prevalence of malnutrition was the highest in hospitals (23.8 %), followed by home-care organisations (21.7 %) and nursing homes (19.2 %). Logistic regression analysis revealed no association with age, time since admission and ward type. Being female was associated with malnutrition only in nursing homes. Blood diseases, gastrointestinal tract diseases, infection, chronic obstructive pulmonary disease, dementia and cancer were the factors associated with malnutrition in hospitals. Dementia was associated with malnutrition in nursing homes, while gastrointestinal tract diseases, diabetes mellitus and cancer were the associated factors in home care. This study shows that malnutrition is still a substantial problem in hospitals, nursing homes and home care in The Netherlands. Malnutrition is a problem for more than one in five patients. Despite growing attention to the problem, more continued alertness is required.