Metabolic disorder contributes to the increase in the mortality rate of patients on hemodialysis (HD). The aim of this study was to estimate the prevalence of metabolic syndrome (MS) and malnutrition in patients on maintenance HD and to evaluate their influence on cardiovascular and all-cause mortality during the follow-up. We carried out a prospective cross- sectional study in which we enrolled 100 patients from a single center who had been followed up for three years. Collected data included demographic characteristics, detailed medical history, clinical variables, MS variables, nutritional status, and laboratory findings. The outcomes were the occurrence of a cardiovascular event and cardiovascular or all-cause mortality during the follow-up period. The Statistical Package for the Social Sciences software was used for statistical analysis. Whereas 50% of patients had MS, 23% showed evidence of malnutrition. Patients with MS were older and had more preexisting cardiovascular diseases (CVDs). All patients were followed for 36 months. During this time, 19 patients with MS and 14 patients without MS died (38% vs. 28%; P = 0.19), most frequently of CVD. Mean survival time was 71.52 ± 42.1 months for MS group versus 92.06 ± 65 months for non-MS group, but the difference was not significant. MS was related with a higher cardiovascular mortality, while malnutrition was significantly associated with all-cause mortality. Our data showed that MS was not related to cardiovascular or all-cause mortality in HD patients and did not influence survival. The independent risk factors for all-cause mortality were older age, preexisting CVD, and malnutrition.