Atrial septal defect is frequently reported with genetic syndromes. But, to the best of our knowledge, it has not been reported with autoimmune polyendocrine syndrome. Here, the case of a 44-year-old-woman with concomitant involvement of the salivary gland, thyroid, intestines, and, possibly endocrine pancreas, diagnosed with autoimmune polyendocrine syndrome type II, is reported with accompanying atrial septal defect. Celiac disease, Hashimoto thyroiditis, and Sjogren syndrome were symptomatic and laboratory confirmed diagnosis; anti-glutamic acid decarboxylase antibody was positive but asymptomatic for type-1 diabetes. She was known to have sinus venosus type atrial septal defect diagnosed at 38 years old, when she had tiredness and chest pain.