The aim of this study was to compare three screening tools for malnutrition in patients with head and neck cancers or central nervous system tumors (CNS) who are undergoing radio-chemotherapy. The study evaluated 124 adult cancer patients. The Subjective Global Assessment (SGA), Mini-Nutritional Assessment (MNA), and Nutritional Risk Screening 2002 (NRS-2002) were chosen to assess the risk of malnutrition. The prevalence of patients at nutritional risk was 31% with SGA, 31% with MNA and 23% with NRS-2002 in all patients. The agreement between SGA and MNA was substantial (k = 0.886, P<0.001); the agreement between SGA and NRS-2002 was moderate (k = 0.713, P<0.001); and the agreement between MNA and NRS-2002 was also moderate (k = 0.795, P<0.001). In subgroup analysis, SGA and MNA substantially (k = 0.973, P<0.001), SGA and NRS-2002 moderately (k =0.722, P<0.001), and MNA and NRS-2002 moderately (k =0.747, P<0.001) agreed in head and neck cancer patients. In CNS tumor patients, SGA and MNA slightly (k = 0.390, P = 0.005), SGA and NRS-2002 fairly (k = 0.457, P = 0.001), and MNA and NRS-2002 substantially (k = 0.878, P<0.001) agreed. The best agreement in tools was observed between SGA with MNA in all patients. Further studies in different tumor groups will enhance our understanding of current tools for malnutrition detection of radiotherapy patient.