Background Primary cardiac spindle cell sarcomas are extremely rare with only a few cases reported. They are frequently misdiagnosed on cardiac magnetic resonance (CMR) imaging as benign myxoma or thrombi and the suspicion of a malignant sarcoma arises only during surgery. This case report describes a case of cardiac spindle cell sarcoma diagnosed after surgery, where the initial diagnostic possibilities included an intramural thrombus and a cardiac myxoma. Case summary A 57-year-old woman was referred to our hospital for evaluation of a possible recurrent myxoma in the left atrium on echocardiography. Cardiac magnetic resonance imaging confirmed these masses as mural thrombotic masses, with a possible remnant of myxoma. After 2 months of anticoagulation therapy, the masses did not decrease in size on CMR imaging, and surgical removal was indicated. The atrial masses were surgically resected together with a large part of the left atrium. Histological examination showed spindle cell sarcoma. Unfortunately, the resection margins were positive and it was not possible to remove more atrium. PET-CT revealed metastasis in the right femur. The patient passed away 1 year after surgery. Discussion The rarity of spindle cell sarcoma and its similarities to benign cardiac myxoma and thrombi on echocardiography and CMR imaging present a diagnostic challenge when evaluating patients pre-operatively. Therefore, a malignant spindle cell sarcoma may only be diagnosed during surgery, after histological examination.