N-terminal pro-brain natriuretic peptide (NT-proBNP) and BNP measurement could have a significant role in differentiating dyspnea between cardiac or pulmonary origin in the emergency room. The development of new and different commercial assays for these B-type natriuretic peptides offers the possibility of improving and simplifying their measurements but this could be defaulted due to the differences in methodology and the lack of assay standardization. We compared four available methods of measuring NT-proBNP and BNP and evaluated their usefulness in diagnosing the causes of breathlessness in the emergency room. The correlation of BNP with different assays was strong with r>0.98 (P<0.0001). Comparison studies between NT-proBNP and BNP procedures were in good agreement with r>0.87. The area under the receiver-operating characteristic curve (ROC) for BNP or NT-proBNP for detecting any cardiac dysfunction was higher than 0.96 (95% CI). A BNP value of 116 pg/mL measurement with the Access BNP assay (Beckman Coulter Inc., Fullerton, CA), a BNP value of 79 pg/mL with Advia Centaur BNP assay (Bayer Diagnostics, Tarrytown, NY), and an NT-proBNP level of 817 pg/mL in Elecsys NT-proBNP assay (Roche Diagnostic, Mannheim, Germany), showed both high sensitivity (>92%) and high specificity (>93%). We have found that NT-proBNP and BNP present similar diagnostic accuracies for the differential diagnosis of dyspnea.