Low-grade B-cell lymphomas of the mucosa-associated lymphoid tissue (MALT) are extranodal tumors that tend to be localized. In this case report, the authors describe an unusual multifocal pulmonary MALT lymphoma, which presented radiologically as three discrete lesions involving two separate lobes of the lung, in addition to numerous separate macroscopic and microscopic foci of disease. The lesions were composed of centrocyte-like cells and cytologically bland plasma cells surrounding reactive lymphoid follicles with focal areas resembling lymphoid interstitial pneumonia (LIP). Immunohistochemical studies demonstrated a predominance of immunoglobulin kappa light chain positive plasma cells in the largest lesion. A polymerase chain reaction (PCR) assay demonstrated conserved immunoglobulin heavy chain gene rearrangements in the large tumor nodules as well as microscopic foci resembling LIP. This case illustrates the utility of PCR for identifying the clonal nature of lymphoid lesions that are too small or heterogeneous to unequivocally assess by other means.