Aim: Early diagnosis of malnutrition is important in hospitalized children. Since the effectiveness of screening tools is still unclear, this study was conducted to assess the risk of malnutrition with PYMS and STRONGkids in inpatients children and to compare them with their anthropometric measurements. Material and Methods: In this cross-sectional study, the risk of malnutrition was determined by PYMS and STRONGkids in 222 patients aged from 1 to 16 years old. Results: According to the BMI values of the patients, 84.7% were normal and 15.3% were acute malnourished. Severe and moderate stunting was detected 8.1% and 11.3% of chronic malnourished patients respectively. In the patients without acute malnutrition, the low malnutrition risk was found 55.0% of the patients with PYMS whereas 42.9% with STRONGkids. The detection rate of the moderate risk with STRONGkids (47.1%) was higher than those PYMS (22.2%). The detection rate of high malnutrition risk with PYMS (22.8%) was higher than those STRONGkids (10.1%). In the patients with acute malnutrition, PYMS could not detect low and moderate malnutrition risk. The detection rates with STRONGkids were 6.1% for low and 36.4% for moderate risk. STRONGkids??? ability to detect patients with high malnutrition risk was lower (58.3%) than that of PMYS (100%). Significant changes were determined between the patients with low, moderate and high malnutrition risk regarding anthropometric measurements by STRONGkids (p<0.001). Conclusions: According to anthropometric measurements, PYMS was superior for detecting acute malnutrition while STRONGkids was superior for detecting chronic malnutrition.