Primary rectal MALT lymphoma is rare comprising less than 1% of MALT lymphomas. A 26-year-old man was referred to our hospital because of constipation and abdominal fullness. Colonoscopy revealed multiple submucosal tumors in rectum. Histopathological examination showed dense proliferation of small lymphoid cells, but lymphoepithelial lesions were not observed. The cells were CD5(-), CD10(-), CD20(+) and cyclinD1(-). The patient was diagnosed as having MALT lymphoma. The patient was negative for API2-MALT1 gene, and radiotherapy was performed and CR was achieved. With the accumulation of cases, establishment of a treatment strategy for primary rectal MALT lymphoma is expected in the future.