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Syncope is a complicated clinical condition involving various diseases. Syncope due to myxoma-like right atrial thrombus is rarely seen in patient without structural heart disease.A 61-year-old ambulant old male visited our emergency department for sudden syncope.After the exclusion of neurological and coronary diseases, a right atrial block mass with a stalk connected to the atrial septum was accidentally found by echocardiography. Pulmonary embolism was subsequently revealed by computed tomographic pulmonary angiography. Atrial myxoma was initially suspected and surgical removal was conducted. Surprisingly, histological examination showed that the pedicled block mass was actually thrombus.The myxoma-like right atrial thrombus and the emboli in the bilateral pulmonary trunks were resected. This patient received anticoagulant treatment with warfarin for 6 months additionally.The patient was successfully discharged and being continually followed.This patient had a past medical history of right femoral neck fracture, which might be responsible for the formation of the myxoma-like right atrial thrombus. We should always consider echocardiography examination in syncope patient at risk of thrombus formation.