Non-Hodgkins lymphoma (NHL) with primary gastrointestinal localization (GI-NHL) represents only 1-4% of the malignant tumors in the gastrointestinal tract. However, the gastrointestinal tract is the most common extranodal site of NHL. The etiology of GI-NHL remains unknown, however, recent studies have shown that infection with viruses like HTLV-1 in the gastrointestinal tract may increase the risk of T cell NHL. The present study was designed to investigate the presence of HTLV-1 genome using PCR on paraffin embedded tissue of primary GI-NHL specimens diagnosed during the period from 1981 to 2003 in the Department of Pathology, Imam Reza Hospital, Mashhad, Iran. The total number of biopsies was 103,573; and 65 cases with primary GI-NHL were found. All these 65 specimens were stained with immunohistochemical markers such as LCA, CD20 and CD3. The presence of HTLV-1 genome was detected in 48 selected patients using tax, LTR, pol and env (GD21) primers.Our results show that male to female distribution was 1.5:1. Most of the patients were in their second) or third decades of life. Eight patients (12.3%) had primary lymphoma in the stomach, 52 (80%) in the small intestine, two (3%) in the large intestine, and three (4.7%) patients had multifocal involvements Eileocecal). According to the Revised European-American Lymphoma (REAL) classification, IPSID lymphoma was the most frequent histologic subtype, comprising 40% of the cases. Sixty-four cases were classified as B cell lymphomas, and one as T-cell lymphoma. Out of 48 specimens which were amplified using PCR, two (4.2%) were positive for HTLV-1. The first case was a 55-year old male with diffuse pleomorphic T cell lymphoma who had a lesion in stomach; and the second case was a 15-month-old female with IPSID lymphoma who had involvement at duodenum.