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Objective: The present study was to compare the incidence of septal defect (SD) in patients with atrial fibrillation (AF) who received radiofrequency ablation or cryoablation. Methods: A total of 293 AF patients were performed with radiofrequency ablation and cryoablation. Cardiac ultrasonography was performed to calculate left atrial diameter (LAD), left atrial ejection fraction (LAEF%), strain rate (SR), left ventricular systolic (SRs), left ventricular diastolic (SRe), and left atrial systole (SRa) before surgery, 3 months and 1 year after surgery. The patients were followed up to observe statin and angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB) medication, AF recurrence, 6-min walk test, stroke, any symptoms caused by arrhythmia, and re-hospitalization. Results: The levels of LAD and SD were higher, while SRe and SRa were lower in the cryoablation group in the comparison with the radiofrequency ablation group after surgery (P<0.05). LAEF was lower in the cryoablation group than the radiofrequency ablation group after 3 months (P<0.05). After 1-year follow-up, no right-to-left shunt occurred in all patients with SD. The AF recurrence rate in SD group was higher than that in the normal group (P<0.05). The use of statin and the application of ACEI/ARB were protective factors, whereas hypertension, LAD, left atrial operation time, and surgical plan were risk factors. Conclusion: SD affects left atrial function and increases the risk of AF recurrence. Hypertension, LAD, and left atrial operation time are risk factors for SD, whereas statin and ACEI/ARB drugs can reduce SD. [ABSTRACT FROM AUTHOR]