Difficulties are often encountered in the diagnosis of malignant lymphoma of the oral and nasal cavities by histology and immunohistochemistry because these malignancies may be complicated by inflammation and necrosis. In the present study, immunoglobulin heavy chain (IgH) and T-cell receptor (TCR) gene rearrangements were examined by the polymerase chain reaction (PCR) in formalin-fixed and paraffin-embedded specimens obtained from 18 patients; the advantages of this method were evaluated. Twelve of these patients were diagnosed as having malignant lymphoma and six had tumors highly suggestive of malignant lymphoma. Fourteen (78%) of the 18 cases were diagnosed as malignant lymphoma histologically and immunohistochemically. Sixteen (89%) of the 18 cases were shown to be monoclonal by PCR. The four cases that could not be histologically or immunohistochemically diagnosed as malignant lymphoma showed monoclonal gene rearrangement by PCR. As a result, six patients suspected of having a malignant lymphoma were diagnosed as having one. The diagnosis of malignant lymphoma by PCR alone still has various problems. However, when the results of PCR are evaluated together with histopathological and immunohistochemical results, PCR makes a useful contribution to the diagnosis of malignant lymphomas of the nasal and oral cavities.