Multiple studies have shown the efficacy and potentially curative effect of catheter ablation (CA). However, CA is always accompanied by a considerable recurrence rate for atrial fibrillation (AF). We hypothesized that pre-procedure assessments of baseline left atrial appendage emptying flow velocity (LAAFV) and N-terminal pro-brain natriuretic peptide (NT-proBNP) levels would help identify abnormal atrial substrate and offer preliminary evidence regarding susceptibility to AF recurrence in patients with paroxysmal or persistent AF, respectively. In 120 patients with AF (paroxysmal, 55; persistent, 65), transesophageal echocardiography was performed with assessment of LAAFV and NT-proBNP was measured before the first AF ablation. After 12 months of follow-up, 16 patients (29.1%) in the paroxysmal AF and 23 patients (35.4%) in the persistent AF experienced recurrence of AF. In ROC analysis, a NT-proBNP value of ae<yen>291 pg/ml in the paroxysmal AF and ae<yen>368 pg/ml in the persistent AF discriminated AFR and non-AFR with the greatest sensitivity and specificity. In multivariate regression analysis, LAAFV (OR 0.88, 95% CI 0.79-0.98, p = 0.023) was identified as an independent predictor of AFR in the paroxysmal AF population post-CA after adjustment for other risk factors; however, in the persistent AF population, LAAFV (OR 0.81, 95% CI 0.68-0.94, p = 0.007) and a NT-proBNP value ae<yen>368 pg/ml (OR 18.29, 95% CI 1.32-252.84, p = 0.030) were identified as independent predictors for rhythm outcome compared to other parameters. In patients with persistent AF, elevated plasma NT-proBNP concentrations combined with low LAAFV were associated with rhythm outcome after AF ablation; however, LAAFV was the only independent predictor of CA efficacy in patients with paroxysmal AF.