Cystic tumor (endodermal heterotopia) of the atrioventricular (AV) node in a 95-year-old female is described. Electrocardiograms showed complete AV blockage with a narrow QRS morphology resulting from the long-standing first degree of AV blockage since age 61. A cardiac pacemaker was implanted at age 83. The patient died of pneumonia at age 95. Autopsy demonstrated a normal heart weight (320 g), normal coronary artery and normal myocardium. Histological examination of the conduction system revealed a marked fibrotic sinoatrial (SA) node and a cystic lesion in the lower right atrium, including the approaches to the AV node. The bundle of His and its branches were completely intact. Cellular nests and cystically dilated tubules were scattered within a loose tissue stroma, which measured 18 × 12 × 5 mm. There were several mitotic figures among the tubules, as well as nuclear fragments similar to apoptotic bodies and exfoliation of the tumor cells. Immunohistochemical studies demonstrated a positive reaction for epithelial membrane antigen, carcinoembryonic antigen, CA19-9, cytokeratin and secretory component in the tubular cells, and a negative reaction for thrombomodulin. Endocrine cells among the tubules were positive only for calcitonin and serotonin. Ultrastructurally, sparse microvilli and desmosome-like structures between the tumor cells were observed. These findings support that this lesion originates from the endoderm. Moreover, it is likely that progression in the degree of AV block may be explained by the cell proliferation activity of the tumor.