BACKGROUND: Hospital malnutrition is an underestimated problem and as many as half of malnourished patients do not receive appropriate treatment. In order to extend the management of malnutrition in health care facilities, multidisciplinary teams focusing on clinical nutrition were established in France. The establishment of such teams within hospital facilities remains nonetheless difficult. We have consequently developed a multifaceted intervention coordinated by a Nutritional Support Team (NST). Our study aims to evaluate the impact of this multifaceted intervention coordinated by a NST, in adherence to recommended practices for the care of malnourished children, among health care workers of a paediatric university hospital. METHODS/DESIGN: We carried out 1) a six-month observational phase focusing on the medical care procedures relative to malnourished children followed by 2) a cluster randomised controlled trial phase to evaluate the impact of a multidisciplinary nutrition team over an 18 month time frame.Based on power analyses and assuming a conservative intracluster correlation coefficient, 1289 children were needed to detect a 25% difference in rates between the two groups of the cluster trial.The implementation of our intervention was coordinated by the NST and had three major components: a) access to a computerised malnutrition screening system associated with an automatic alert system, b) an awareness campaign directed toward the health care workers and c) a leadership based strategy.Main outcomes included the number of daily weighings during hospitalisation, the investigation of malnutrition etiology and the management of malnutrition by a dietician and/or the NST.Due to the clustered nature of the data with children nested in departments, a generalized estimated equations approach will be used to analyse the impact of the multifaceted intervention on primary and secondary outcomes. DISCUSSION: Our results will provide an overall response regarding the effectiveness of our multifaceted intervention and we should be able to suggest an organization and mode of operation of NST. TRIAL REGISTRATION: ClinicalTrials.gov: NCT01081587.