Brain natriuretic peptide (BNP) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) are currently used for the diagnosis, prognosis, and therapeutic decision making in heart failure patients. The aim of the study was to compare BNP and NT-proBNP plasma concentration profiles in 42 patients with decompensated heart failure who underwent treatment in the emergency department. A significant decrease in both peptide concentrations fell beyond 24 hours of therapy. BNP concentration underwent a more responsive change from admission (-54.1%+/-8.6% at 72 hours and -57.4%+/-7.6% at discharge) than NT-proBNP concentration (-17.6%+/-5.4% at 72 hours and -18.6%+/-5.6% at discharge). Although BNP and NT-proBNP concentrations were highly correlated, no correlation in their variations was found, a finding that suggests a different kinetic behavior in response to treatment. Sequential measurements of BNP and NT-proBNP provide a reliable marker to confirm clinical improvement after 24 hours of treatment. BNP may show some advantages over NT-proBNP as a more sensitive marker of early stabilization in response to therapy.