Background: N-terminal pro-brain natriuretic peptide (NT-proBNP) has been demonstrated to be associated with cardiovascular disease (CVD) and mortality in end-stage renal disease patients. We hypothesized that common confounders, such as protein-energy wasting (PEW) and inflammation could modulate this relationship. Methods: NT-proBNP was measured in 222 prevalent hemodialysis (HD) patients (55.4% male, mean age 66 years, range 51–74) using commercial ELISA. Levels were related to clinical characteristics, biochemical markers and survival. Results: NT-proBNP levels were positively associated with IL-6 (ρ = 0.37, p <0.001) and C-reactive protein (ρ = 0.25, p <0.001), but negatively associated with serum IGF-1 (ρ = –0.34, p < 0.001), handgrip strength (ρ = –0.30, p <0.001) and body weight (ρ = –0.20, p < 0.001). In multivariate analysis, an NT-proBNP level above the cutoff of the receiver-operating curve (9,761 pg/ml) was associated with PEW (odds ratio = 2.30, p = 0.008) even following adjustment for age, dialysis vintage, inflammation and the Davies score. As expected, NT-proBNP predicted clinical CVD (odds ratio = 1.90, p = 0.05) and all-cause mortality (Cox regression hazard ratio = 1.57, p = 0.03) also after adjustment for confounders. Patients with an NT-proBNP above the cutoff also exhibited a higher mortality (Kaplan-Meier χ2 = 13.95, p < 0.001). Conclusion: We demonstrate a novel association between NT-proBNP and PEW, which may be part of the explanation for the strong links between NT-proBNP and mortality in HD patients.