Pyothorax-associated lymphoma (PAL) is a unique lymphoma developing in the pleural cavity after long-standing pyothorax. They are diffuse large B-cell lymphomas (DLBCLs), frequently with immunoblastic morphology, and show a strong association with Epstein-Barr virus (EBV) infection. In this study, cDNA microarray analysis was performed in six cases with PAL and 12 with nodal DLBCL. Among 5516 informative genes, 348 displayed more than 2-fold difference (higher or lower) of expression level between PAL and nodal DLBCL (P < 0.001). These genes are known to be involved in apoptosis, interferon response, and signal transduction. One of the most differentially expressed genes, IFI27 (interferon-alpha-inducible protein 27) was subjected to quantitative RT-PCR analysis, and increased expression of IFI27 was confirmed. Overexpression of IFI27 was also found in cell lines derived from PAL, but not in other lymphoid cell lines. This study shows that PAL is a distinctive subtype of DLBCL not only in its clinical presentation, but also in its molecular profile.