Abstract The utility of B-type natriuretic peptide (BNP) testing in patients with atrial fibrillation (AF) is poorly defined. We analyzed patients ( n = 452) included in the BNP for Acute Shortness of Breath Evaluation (BASEL) study. Patients were randomly assigned to a diagnostic strategy with or without the use of BNP. Ninety-nine patients presented with AF ( n = 48 BNP group; n = 51 control group). Although comparable with respect to gender and cardiopulmonary comorbidity, patients with AF were older and more often had heart failure as the cause of dyspnea. In addition, patients with AF had higher in-hospital mortality (13% versus 6%, P = 0.012). The use of BNP significantly reduced time to discharge (BNP group median 8 days 1–16 versus 12 days IQR 4–21 control group; P = 0.046) in patients with AF. Initial total treatment costs (median) were $4239 769–7422 in the BNP group and $5940 4024–10848 in the control group ( P = 0.041). These benefits were maintained after 90 days: patients in the BNP group had spent fewer days in hospital (10 days 2–21 versus 15 days IQR 9–27; P = 0.022) and induced lower total treatment costs ($4790 1260–9387 versus $7179 4311–13173; P = 0.016). In conclusion, the use of BNP seems to improve the management of patients with AF presenting with dyspnea.