Paediatric in-patients are at high risk of malnutrition but validated paediatric screening tools suitable for use by nursing staff are scarce. The present study aimed to assess the diagnostic accuracy of the new Paediatric Yorkhill Malnutrition Score (PYMS). During a pilot introduction in a tertiary referral hospital and a district general hospital, two research dietitians assessed the validity of the PYMS by comparing the nursing screening outcome with a full dietetic assessment, anthropometry and body composition measurements. An additional PYMS form was completed by the research dietitians to assess its inter-rater reliability with the nursing staff and for comparison with the Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP) and the Paediatric Subjective Global Nutritional Assessment (SGNA). Of the 247 children studied, the nurse-rated PYMS identified 59% of those rated at high risk by full dietetic assessment. Of those rated at high risk by the nursing PYMS, 47% were confirmed as high risk on full assessment. The PYMS showed moderate agreement with the full assessment (kappa = 0.46) and inter-rater reliability (kappa = 0.53) with the research dietitians. Children who screened as high risk for malnutrition had significantly lower lean mass index than those at moderate or low risk, but no difference in fat. When completed by the research dietitians, the PYMS showed similar sensitivity to the STAMP, but a higher positive predictive value. The SGNA had higher specificity than the PYMS but much lower sensitivity. The PYMS screening tool is an acceptable screening tool for identifying children at risk of malnutrition without producing unmanageable numbers of false-positive cases.