Idiopathic bilateral atrial dilatation (IBAD) is an extremely rare anomaly and is usually associated with atrial fibrillation. Plasma levels of atrial natriuretic peptide (ANP) have been shown to increase in patients with atrial fibrillation. However, secretion of ANP and brain natriuretic peptide (BNP) in patients with IBAD remains unclear. We investigated the clinical features of 9 patients with IBAD and 16 age- and sex-matched patients with lone atrial fibrillation (LAF). Plasma levels of ANP and BNP were measured, and echocardiographic parameters were followed. Left (LAV) and right atrial volumes (RAV) were significantly higher in patients with IBAD than in patients with LAF (both p < 0.01). There were no differences between patients with IBAD and LAF in other echocardiographic parameters. The percent increases in LAV and RAV in patients with IBAD exceeded those in patients with LAF (both p < 0.01). Plasma levels of BNP and the BNP/ANP ratios in patients with IBAD were significantly higher than those in patients with LAF (both p < 0.01), but there was no significant difference in plasma levels of ANP. Regarding the clinical course of the patients with IBAD compared with those with LAF, the atrial volume increased gradually, and plasma levels of BNP were significantly higher. These findings suggested that IBAD was not only influenced by long-term atrial fibrillation, but also by subclinical left ventricular dysfunction.