Primary rectal mucosa-associated lymphoid tissue (MALT) lymphoma is a particularly rare disease, comprising <1% of gastrointestinal lymphomas. Although antibiotic therapy has been demonstrated effective for gastric MALT lymphoma, the optimal treatment for MALT lymphoma of the rectum is unknown. Radiotherapy or surgery is often used to treat limited stage MALT lymphoma of the rectum. Here, we describe a case of a 44-year-old-man, who was diagnosed with primary MALT lymphoma of the rectum through colonoscopy. Other staging evaluations, including upper gastrointestinal endoscopy, abdomino-pelvic CT, chest CT, 18F fludeoxyglucose-positron emission tomography, and a bone marrow examination showed no other abnormalities, except stage IA para-rectal lymphadenopathy. The patient received 2 months of radiotherapy without major toxicity. A follow-up abdomino-pelvic CT scan revealed marked improvement in the volume of rectal lymphoma and adjacent lymph nodes. Mucosal nodularity of the lower rectum had completely regressed at the follow-up endoscopy and complete remission was confirmed with a biopsy.