Gastrointestinal stromal tumors (GISTs) are primarily mesenchymal tumors with specific histological features found in the gastrointestinal tract and the abdomen. They are identified and diagnosed by the expression of the protooncogene protein called CD117 detected using immunohistochemistry. Atrial myxoma is the most common benign primary tumor of the heart. Carney triad is considered to be a specific type of multiple endocrine neoplasia. Three classically related tumors are the GIST, pulmonary chondroma, and extra-adrenal paraganglioma. Carney syndrome is an autosomal dominant syndrome with multiple components, characterized by myxomatous neoplasms (cardiac, endocrine, cutaneous, and neural), pigmented lesions of the skin and mucosae, and multiple endocrine tumors.The patient in this study was a 75-year-old man with no known illness. He had a tumor in the stomach and was operated. The pathology was reported as low-grade GIST; therefore, adjuvant imatinib treatment was not recommended. Further, owing to the shortness of breath in the third month of follow-up, echocardiography was requested. Left atrial mass was detected and operated. His pathology was compatible with atrial myxoma. After both operations, the patient is still being followed up in remission in our clinic.Only one case has been reported worldwide documenting the coexistence of atrial myxoma and GIST, and none has been seen in Turkey. Thus, to the best of our knowledge, this is the second case in the literature and first report from Turkey.