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Background: It was previously reported, based on a retrospective study, that preliminary removal of air bubbles in heparinized saline water with extracorporeal balloon inflation reduced the incidence of asymptomatic cerebral embolism (ACE). The present study aims to compare the incidence of ACE between a conventional and pre-inflation method during cryoballoon ablation in a prospective randomized controlled study. Methods: A total of 98 atrial fibrillation patients were enrolled and randomized into conventional and pre-inflation groups. Patients in the pre-inflation group received balloon massaging with preliminary extracorporeal balloon inflation in saline water before the cryoballoon was inserted into the body. Results: The baseline characteristics were similar between the two groups. Post-procedural 3-Tesla MRI revealed CE in 27.6% of patients. Symptomatic CE only occurred in two patients in the pre-inflation group. One patient had transient dysarthria and mild muscle weakness in one hand; the other patient complained of transient left upper limb weakness, left lower limb paresthesia and dysarthria. The incidence of ACE detected by cerebral MRI did not differ between the two groups to a statistically significant extent (conventional vs. pre-inflation; 22.9% vs. 29.2%; P = 0.49). In the multivariable analysis, eGFR was independently associated with the presence of ACE (odds ratio 0.95; 95% confidence interval 0.907–0.995; P = 0.03). Conclusion: In this prospective randomized study, the preliminary removal of air bubbles in heparinized saline water with extracorporeal balloon inflation had no impact on the incidence of ACE.