A higher body mass index is associated with better outcomes in hemodialysis patients; however, this index does not differentiate between fat and muscle mass. In order to clarify this, we examined the relationship between measures of fat and muscle mass and mortality in 1709 patients from the Hemodialysis Study. Triceps skin-fold thickness was used to assess body fat and mid-arm muscle circumference was used to assess muscle mass. Cox regression was used to evaluate the relationship between measures of body composition with all-cause mortality after adjustments for demographic, cardiovascular, dialysis, and nutrition-related risk factors. During a median follow-up of 2.5 years, there were 802 deaths. In adjusted models with continuous covariates, higher triceps skin-fold thickness and higher body mass index were significantly associated with decreased hazards of mortality, while higher mid-arm muscle circumference showed a trend toward decreased mortality. In adjusted models, lower quartiles of triceps skin-fold thickness, mid-arm muscle circumference, and body mass index were all significantly associated with higher all-cause mortality. These studies show that body composition in end-stage renal disease bears a complex relationship to all-cause mortality.