We report the successful application of gene rearrangement analysis to the lymphocytes obtained by bronchoalveolar lavage (BAL) for the diagnosis of pulmonary malignant lymphoma. A 45-yr-old female patient who had been suffering from back pain was shown to have macroglobulinemia and pulmonary infiltrative shadow by chest radiography. Transbronchial lung biopsy revealed a small B-cell infiltrate with monotypic immunoglobulin expression (IgM/kappa light chain), and malignant lymphoma was highly suspected. BAL was performed to evaluate the cell profiles. The phenotyping of lavaged lymphocytes by flow cytometry revealed that the major component of the lymphocytes was CD3-positive T cells, and that CD21-positive B cells accounted for only 10% of all lymphocytes. This result was contradictory to the immunohistochemical population of lymphocytes in biopsied specimens. However, gene analysis of lavaged lymphocytes revealed positive immunoglobulin heavy chain rearrangement and negative immunoglobulin light chain and T-cell receptor rearrangement, suggesting that B cells making up a minor population of lavaged lymphocytes were proliferating monoclonally. Thus, in this case, gene analysis was an effective procedure for detecting the origin of tumor cells and distinguishing monoclonality from reactive accumulations. To our knowledge, this case represents the first reported application of gene rearrangement analysis to cells obtained by BAL. The sensitivity and usefulness of this analysis for the accurate evaluation of pulmonary lymphoproliferative lesions, when applied to BAL cells, should be emphasized.