Gastrointestinal tracts are the most frequently involved sites of mucosa-associated lymphoid tissue (MALT) lymphoma. Stomach is the most common site of involvement among the gastrointestinal tract. Simultaneous occurrence of primary gastric and colonic MALT lymphoma is rarely reported. We report a case of synchronous double primary MALT lymphoma of the colon and stomach in a healthy subject. A 62-year-old male underwent an esophagogastroduodenoscopy and colonoscopy for medical checkup. An endoscopic examination of the stomach showed an erythematous mucosa in the great curvature of the lower body. The endoscopic finding of the colon was a flat elevated lesion in the sigmoid colon. Microscopic examinations revealed MALT lymphoma and gastric Helicobacter pylori infection. We performed imaging studies to evaluate distant metastasis and confirmed that there is no other metastasis. The patient was treated with H. pylori eradication therapy and CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) chemotherapy. He had not experienced any recurrence since the treatments, and reached a complete remission state after six months.