Background Assessing thromboembolic risk is important for patients with atrial fibrillation. The use of new scanning techniques in clinical practice has not been sufficiently investigated. This study aimed to determine the efficacy of left lateral decubitus computed tomography for diagnosing left atrial appendage (LAA) thrombus as a screening tool before catheter ablation and to evaluate the risk factors for thrombus formation. Methods This retrospective cohort study included 101 patients. All patients underwent transthoracic echocardiography (TTE) and left lateral decubitus cardiac computed tomography (CT). Transesophageal echocardiography (TEE) was provided only to confirm the LAA thrombus. Patients with allergic reactions to iodide, increased creatinine levels, hyperthyroidism, pregnancy, and age < 18 years were excluded. The CHA2-DS2-VASc and HAS-BLED scores were calculated in each patient. Results All LAA thrombi detected on CT were confirmed on TEE. Higher CHA2-DS2-VASc, HAS-BLED scores, enlarged left atrium, and the anteroposterior dimension of the left atrium were significantly associated with LAA thrombus. An LAA cauliflower shape is a predictor of LAA thrombus. An increase of LAA volume by 1 cm3 increases the chances of LAA thrombus and cerebral infarct by 2%. The growth of the LAA anteroposterior size by 1 cm increases the risk of LAA thrombus by 2.9 times and of cerebral infarct by 78%. An increase in the CHA2DS2-VASc score by 1 point increases the risk of thromboembolism and cerebral infarction by 12%. Conclusion Cardiac CT with the patient positioned on the left side is a good screening tool to determine LAA thrombus and provides highly useful information for predicting thrombosis formation risk in LAA.