Gastric yolk sac tumors are extremely rare with only a few cases reported in the literature. Here, we present the case of a 50-year-old man with an adenocarcinoma and a yolk sac tumor of the stomach, without metastasis to the lymph nodes. The tumor was an early gastric carcinoma confined to the submucosa. Twelve months post-operation the patient was alive with no complications. The yolk sac tumor showed positive labeling for alpha-fetoprotein (AFP), alpha1-antitrypsin (alpha1-AT), cytokeratin (CK) and carcinoembryonic antigen (CEA), but was negative for human chorionic gonadotrophin (hCG), placental alkaline phosphatase (PLAP), epithelial membrane antigen (EMA) and p53. The adenocarcinoma was positive for alpha1-AT, CK, EMA, and CEA, but was negative for AFP, hCG, PLAP, and p53. These findings suggest that the yolk sac tumor and the adenocarcinoma components are closely related and may represent distinct phenotypes that arise from a common mucosal epithelial cell.