A 17.5-year-old boy, previously treated in a nephrology clinic due to chronic proteinuria, was referred for a routine cardiology consultation before being transferred to an adult clinic for further care. Physical examination and echocardiography showed no circulatory abnormalities and normal blood pressure, while echocardiography revealed an abnormal tumour-like structure measuring 1.3 × 1.5 cm in the left atrium, remaining in contact with the interatrial septum. Continuous infusion of heparin was started, after which no change in tumour size was obtained. The diagnosis was extended to include computed tomography, which showed a soft 1.5 × 2.1 × 2.1 cm tissue structure connecting with the interatrial septum with uneven contours, and magnetic resonance imaging, which indicated that the left atrial structure corresponded to myxoma, and the presence of enhancement spoke against the suspicion of a thrombus, although the presence of a small thrombus on the tumour could not be clearly excluded. The boy was qualified for a cardiac surgery, during which the pathological structure was removed and then sent for histopathological analysis, which revealed a heart tumour with myxoma. After the surgery, the patient was transferred to the department of paediatric cardiology for further treatment, where he received enoxaparin sodium, antibiotics and acetylsalicylic acid. After a few days, an about 1 cm layer of fluid appeared in the pericardium, which regressed after the incorporation of ibuprofen and dehydrating agents. After 2 weeks, the boy was discharged home in good condition, with a recommendation to continue care at a nephrology, cardiology and genetic clinic due to MTHFR mutation, which may be associated with hereditary hypercoagulability, detected during hospital stay.