Primary cardiac tumors are known to be rare. Of the benign primary tumors, rhabdomyoma predominates in neonates and infants. Tuberous sclerosis is found in hall of the patients with rhabdomyomas. Rhabdomyomas demonstrate benign pathological characteristics and may regress spontaneously that resection of the intracavitary obstructing portion of these tumors are recommended. We performed resection of intraatrial rhabdomyoma which had been obstructing mitral valve orifice and caused heart failure in a neonate. Postoperatively, fungal endocarditis developed and after 3 days, rapid growth and extension of the vegetation in the aorta obstructed the flow through the ascending aorta and resulted in hemodynamic deterioration.