Background: Cardiac myxoma is the most common primary heart tumor but is rarely found in the pediatric population. The classic triad present in most patients includes embolism, intracardiac obstruction, and constitutional symptoms, although occasional patients have no symptoms. Myxoma might not be the first thought in a child who presents with gastrointestinal symptoms. However, with appropriate clinical suspicion, prompt diagnosis and successful surgical resection are possible. Case: A 3-year-old boy who presented with diarrhea, vomiting and abdominal pain over a 4-day period was transferred to our hospital for evaluating cardiac murmur and admitted. He had complained of abdominal pain and shortness of breath and was treated for gastroenteritis at a outside hospital. He was diagnosed with microcytic hypochromic anemia 10 days before admission and had been taking a iron medication. On physical examination, heart rate was 152/min and blood pressure was 118/91 mmHg. A grade 2/6 regurgitant murmur was heard on apex and P2 sound was accentuated. The lungs were clear and liver was not palpable. A chest x-ray showed slight cardiomegaly and left atrial enlargement. Electrocardiogram showed atrial dilatation and biventricular hypertrophy. Transthoracic echocardiography demonstrated a huge(25–30mm), pedunculated and fragile mass in the left atrium, arising from interatrial septum and impinging on the mitral valve annulus causing mitral regurgitation. On laboratory tests, white blood cell count was 9800/mL with 51.1% segmented neutrophils. C-reactive protein level was 4.2 mg/dL. Cardiac biomarkers were as follows: creatine phosphokinase, 65 U/L; creatine kinase MB, 1.2 ng/mL; Troponin I, 0.421 ng/mL; pro-B-type natriuretic peptide, 1577 pg/mL. Renal function tests and serum electrolyte levels were normal. He was scheduled for urgent operation. Brain MRI showed multiple small scattered lesions with diffusion restriction in white matter and cortex of right cerebral hemisphere, suggesting thromboembolic cerebral infarction. He had excision of myxoma on the 2nd day of hospitalization and was discharged on 13th day. Conclusion: We report the case of a left atrial myxoma in a 3-year-old boy who presented with gastrointestinal symptoms.