Pyothorax-associated lymphoma was found in a man who had a history of collapse therapy for pulmonary tuberculosis about 50 years ago. An autopsy specimen revealed histology of diffuse large B-cell lymphoma with latency III Epstein-Barr virus (EBV) infection. However, an open biopsy 2 years and 7 months before death showed a polymorphic appearance with abundant T-lymphocytes. Most of the EBV-infected atypical lymphocytes did not express either B- or T-cell markers as far as examined in the paraffin-embedded biopsy specimen, and rearrangements of immunoglobulin and T-cell receptors were not found. It seemed difficult to diagnose a B-cell lymphoma at the time of biopsy. However, retrospectively considered, if a phenotype of EBV-infected atypical lymphocytes is uncertain in cases showing polymorphic appearance, it might be better to consider the future evolution to overt B-cell lymphoma. Since pyothorax-associated lymphoma shows latency III infection of EBV, at least the immunohistochemistry of EBNA-2 and LMP-1 seems helpful for the diagnosis to prove which cells are infected by EBV.