An autopsy case of a primary malignant tumor of the heart in a 15‐year‐old boy was reported. The tumor had possibly arisen from the subendocardial region of the septal area of right atrium, occupied the atrial septum and formed a spherical mass with a diameter of ca. 9 cm. It protruded into the right atrial chamber and ruptured the endocardium. Multiple metastases were observed in the lungs and the paratracheal lymph nodes. On the basis of light and electron microscopic features, the tumor was interpreted as a poorly differentiated mesenchymal tumor with partial myxosarcomatous differentiation. The histogenetical aspects of this tumor were discussed with reference to morphology and cytodifferentiation of primitive mesenchymal tissues of the he