Gene rearrangement is an important diagnostic marker of malignant lymphoma, and rearrangements of the immunoglobulin heavy chain (IgH) and T-cell receptor gamma chain (TCRgamma) genes are useful markers for Band T-cell lymphoma, respectively. A polymerase chain reaction (PCR) can be used to analyze clonality in formalin-fixed paraffin-embedded specimens. We performed 73 monoclonal analyses of such specimens of lymphoma tissues and examined the ability to diagnose malignant lymphoma by this method. Monoclonality of lymphoma cells was found in 71.9% and 78.9% of specimens with IgH and TCRgamma gene rearrangements, respectively. Therefore, in diagnosing cases of non-Hodgkin lymphoma in which neoplasms and reactive lymphoid tissues are difficult to identify by morphological and immunohistochemical findings, PCR-based monoclonal analysis may allow confirmation of a pathological diagnosis of malignant lymphoma.