Protein-energy wasting in hemodialysis (HD) patients is characterized by decreased skeletal muscle mass and plasma protein. Some previous studies reported relationships between skeletal muscle dysfunction and iron deficiency. Dialysis patients with malnutrition may have a functional iron deficiency (FID) because of inflammation. Serum total iron binding capacity (TIBC), correlated with transferrin, is a nutritional status marker in HD patients and a biomarker of iron status. The relationship between muscle loss and iron status is unknown. The aim of the present study was to assess the relationship between iron status and change in skeletal muscle mass. A prospective cohort of 267 HD patients was examined for 12months. Blood samples were obtained at baseline to measure TIBC, ferritin, transferrin saturation (TSAT), and hepcidin-25. Nutritional status and changes in muscle mass were assessed by subjective global assessment, albumin, creatinine index, and percentage creatinine generation rate. At baseline, lower tertiles of TIBC were significantly related to lower muscle mass and albumin levels; they were also significantly correlated with high ferritin, hepcidin-25, and TSAT levels, as well as a higher proportion of use of erythropoiesis-stimulating agents. Multiple regression analysis adjusted with confounders showed TIBC was an independent biomarker for decreased muscle mass and albumin. Change in muscle mass remained significantly decreased in the lower tertile of TIBC and in malnourished patients. The present study demonstrated relationships between FID and muscle loss. TIBC was an independent biomarker of muscle loss in HD patients, considering iron status, inflammation, oxidative stress, and malnutrition.