Splenic marginal zone cell lymphomas (SMZCLs) are low-grade B-cell lymphomas that usually present with massive splenomegaly and subtle (subleukemic) peripheral blood involvement. Polymerase chain reaction (PCR) analysis of peripheral blood from a patient with subleukemic SMZCL showed evidence of two clonal immunoglobulin heavy chain (IgH) gene rearrangements. IgH PCR analysis of DNA derived from the patient's splenic neoplasm demonstrated a single clonal IgH rearrangement, which had a different electrophoretic mobility from either of the two PCR products detected in the patient's peripheral blood. Additional characterization of these PCR products by DNA sequencing demonstrated two independent IgH rearrangements in the peripheral blood, one of which used IgH joining region 6c (JH6C) and the other JH4. A different IgH rearrangement was present in the splenic tumor, which used JH4a. No sequences from the splenic neoplasm were detected in the peripheral blood and vice versa. This case illustrates that PCR might reveal monoclonal populations in peripheral blood unrelated to the presence of lymphoma in other anatomic compartments.