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Background Air embolus penetrating into heart chamber as a complication during percutaneous radiofrequency catheter ablation has been infrequently reported. Case presentation A 55-year-old man with dextrocardia who suffered from abdominal pain was suspected to have multiple arterial thromboembolisms, which might have originated from left atrium thrombosis since he had atrial fibrillation. He received oral anticoagulant therapy and catheter ablation of the arrhythmia. During the ablation procedure, an iatrogenic aeroembolism penetrated into the left atrium due to improper operation. Ultimately, the entire air embolus was extracted from the patient, who was free of any aeroembolism events thereafter. Conclusions It is essential for an operator to pay full attention to all details of the procedure to avoid an aeroembolism during catheter ablation. In case of aeroembolism, removal by aspiration is an optimal and effective treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12872-017-0581-7) contains supplementary material, which is available to authorized users.