ABSTRACT. We evaluated the usefulness of polymerase chain reaction for antigen receptor gene rearrangement analysis (PARR) of endoscopic biopsy specimens for diagnosis of canine alimentary lymphoma. Two endoscopic biopsy specimens were obtained from each lesion in 78 dogs with gastrointestinal symptoms. One specimen was histopathologically examined by a pathologist, and the other was analyzed by PARR. All samples were categorized into three groups [lymphoma (n=4), adenocarcinoma (n=5) and enteritis groups (n=69)] based on the histopathological diagnosis. In the lymphoma group, one case was IgH major-positive, and three cases were TCR-positive, representing clonal expansion of B-and T-cells, respectively. PARR produced negative results for all cases in the adenocarcinoma group. In the enteritis group, six cases were TCR-positive. Two of the six TCR-positive enteritis cases were cytologically diagnosed as lymphoma by fine needle aspiration during a laparotomy. In the enteritis group, the survival times were compared between the TCR-positive and TCR-negative cases. The overall survival time of the TCR-positive enteritis cases was significantly shorter than that of the TCR-negative enteritis cases according to a log-rank test (p<0.0001). With regard to other factors, such as age, clinical signs and the serum albumin concentration, there were no significant differences between the TCR-positive and TCR-negative enteritis cases. In conclusion, PARR is capable of detecting alimentary lymphoma and latent alimentary lymphoma, which cannot be histopathologically diagnosed using endoscopic biopsy specimens. Furthermore, a TCR-positive result in PARR may imply a poor prognosis.