To investigate the clinicopathological characteristics and optimal treatment modalities of primary non-Hodgkin lymphoma (NHL) in the small and large intestine. Forty patients with primary NHL in the small and large intestine were studied retrospectively. All cases were reclassified according to the World Health Organization (WHO) classification of lymphoma in 2001. Fourteen patients had primary disease in the small intestine, which were all of B-cell origin with diffuse large B-cell lymphoma (DLBCL) diagnosed in 5 of 14 (35.7%) patients and mucosa-associated lymphoid tissue (MALT) lymphoma in 8 of 14 (57.1%) patients. Ileum was the most commonly involved site (8 of 14 patients, 57.1%), followed by jejunum (2 of 14 patients, 14.3%) and duodenum (1 of 14 patients, 7.1%). Twenty-five patients had primary colorectal lymphoma, with B-cell origin accounting for 92.0% and T-cell origin for 8.0% of these patients. The ileocaecal region has the highest involved rate (13 of 25 patients, 52.0%), followed by colon (7 of 25 patients, 28.0%) and rectum (3 of 25 patients, 12.0%). Compared with surgery alone, post-operation chemotherapy or chemoradiotherapy can significantly improve DLBCL patients' event-free survival (EFS). However, no post-operation treatment modality can improve OS or EFS for patients with MALT lymphoma. B-cell lymphoma is the most common pathological type of intestinal lymphomas. Chemotherapy-containing treatment modality is an effective way to improve intestinal lymphoma patients' EFS, especially for those with DLBCL subtype.