Our study aims at determining whether the efficiency of step-wise catheter ablation (step-CA) of persistent atrial fibrillation (pAF) can be tracked using organization indices based on the harmonic components of atrial ECG signals until pAF termination. ECG time series devoid of QRST were recorded at baseline (pre-ablation), after pulmonary vein isolation and at the end of left atrium (LA) ablation. Using adaptive harmonic frequency tracking schemes, two organisation indices characterizing the relationship between the harmonic components of atrial ECG were computed. Patients in whom the pAF termination was achieved during ablation within the LA displayed greater baseline atrial ECG organization that further increased significantly at the end of LA ablation as opposed to patients in whom the pAF did not terminate. Estimation of the level of atrial ECG organization based on adaptive harmonic schemes appears as promising tool for tracking changes in pAF dynamics during CA and prediction of procedural outcome.