Early recurrence of atrial fibrillation (ERAF) after catheter-ablation (CA) can be a transient phenomenon due to inflammation, or a harbinger of late AF recurrence due to CA lesion (re)conduction. We studied the relationship between ERAF and the 3-month CA lesions integrity. Forty one consecutive AF patients who underwent a pulmonary vein isolation (PVI), roof line (RL) and mitral isthmus line (MIL) CA were enrolled. At 3 months all patients underwent invasive assessment of the lesion set integrity irrespective of ERAF. The PVI, RL and MIL ablation was successful in 100.0%, 95.1% and 82.9% patients, respectively. At the 3-month remapping, a gap in PVI-lesion(s), RL or MIL was identified in 61.0%, 31.7% and 36.6% patients, respectively. Patients with (n = 17, 41.5%) compared to those without ERAF (n = 24) had a significantly higher rate of any PV-reconnection (88.2% vs. 41.7%), the right PV(s)-reconnection (82.5% vs. 29.2%) and the RL gap (52.9% vs. 16.7%), as well as a higher number of reconnected right PVI-segments, all p < 0.05. On multivariate analysis, only the number of reconnected right PVI-segments was associated with ERAF (OR 4.26, p = 0.004). The ERAF following PVI + RL + MIL ablation was significantly related to 3-month PV-reconnections and the presence of RL gaps.