The objective is to investigate the association between pathological type and clinical features, response to treatment and prognosis of primary gastrointestinal Non-Hodgkin's lymphoma (PGINHL). The clinicopathologic features, response to treatment and survival of 124 patients with PGINHL, were investigated retrospectively. Ninety-one patients were treated with surgery, most of which included combined therapy, while 32 patients received chemotherapy alone. Survival analysis was performed by Kaplan-Meier and Cox regression method. The most common immunophenotype was B-cell subtype. In 115 (92.7%) patients of B-cell lymphoma, mucosa-associated lymphoid tissue lymphoma (MALToma) and diffuse large B-cell lymphoma (DLBCL) were 55 and 50 patients, respectively. The patients of two pathological types had different clinical features including stage, B symptoms, sites of tumor, distant involvement, International Prognosis Index Score, size of tumor, and response to treatment. Both overall survival curve and multiple Cox regression analysis indicated that pathological type was statistically significant. The pathological subtype of PGINHL was an important prognostic factor. The patients with MALToma appear to have more favorable prognosis than those with DLBCL.