Malnutrition is a relatively common problem in patients on hemodialysis (HD) and is associated with increased morbidity and mortality in affected patients. With the aid of subjective global assessment (SGA), a semi-quantitative scale for estimating nutritional status, the malnutrition score (MS), has been developed. The MS incorporates advantages of the SGA while extending the reliability and precision. This study was performed to assess the nutritional status in patients on HD at the Mostafa Khomeini Hospital, Tehran, Iran. Based on the MS, which consists of seven components--weight change, dietary intake, gastrointestinal (GI) symptoms, functional capacity, comorbidity, subcutaneous fat, and muscle wasting--we conducted a cross-sectional descriptive-analytic study on 54 HD patients (35 males, 19 females) with age range of 18 to 82 years (mean 44.2 +/- 19.8 years). Each component of the MS has a score from one (normal) to five (very severe). Anthropometric measurements including triceps skin-fold thickness (TSF), mid-arm circumference (MAC) and mid-arm muscle circumference (MAMC) were taken on all patients. Also, the body mass index and TSF/MAC ratio were calculated. Relevant laboratory parameters were checked. The duration of HD of the study patients ranged between 5 and 36 months (mean 19.5 +/- 1.5 months). Data analysis was carried out using the SPSS, Pearson correlation, 't' test and regression. Based on the MS, 40.7% of patients had malnutrition (mean score 13.8 +/- 2.8). There were statistically significant correlations between TSF (p < 0.01), MAC (p = 0.02), MAMC (p = 0.01), TSF/MAC ratio (p < 0.001), BMI (p = 0.028), serum albumin concentration (p = 0.021) and MS. No statistically significant correlation was found between the MS and urea reduction ratio, protein catabolic rate, age, gender, or duration of dialysis. After 1 year, 20.4% of patients died because of dialysis-related complications. The mortality rate did not show significant correlation with age, presence of diabetes mellitus, biochemical parameters, and anthropometric measures. A significant correlation was found between the protein catabolic rate (nPCR) and the mortality rate (regression analysis, p = 0.016); lower values of nPCR were associated with increased mortality. Our study suggests that the MS is a reliable, precise, and rapid method for estimating the nutritional status in patients on HD. The nPCR can be used as a predictor of increased mortality. Further studies with larger sample size and longer duration are required to confirm this observation.