Rearranged immunoglobulin heavy chain (IgH) genes provide unique clonal markers for B cells. Since amplification of the rearranged gene by polymerase chain reaction (PCR) and demonstrating that the amplified sequence is indeed derived from tumor cells is more problematic in non-Hodgkin's lymphoma (NHL) than in other B cell malignancies, we used a comprehensive PCR primer set and formulated stringent selection criteria to identify tumor-specific rearranged IgH genes. Rearranged IgH genes amplified from lymphoma DNA were considered to be of tumor origin if they were monoclonal, and if the same rearrangement was amplified with at least two independent VH-specific primers. From 11 of 13 (85%) intermediate- and high-grade malignant NHL, IgH rearrangements were isolated. Intraclonal IgH sequence heterogeneity was studied in four lymphomas, and detected in two of them. PCR using a lymphoma-specific primer followed by Southern hybridization of PCR product with a specific probe allowed detection of lymphoma DNA after 10,000-fold dilution. Circulating lymphoma cells were detected in patient blood and bone marrow samples which were negative by morphological and immunological criteria. Thus, also in intermediate- and high-grade malignant lymphoma, sensitive minimal disease detection using the rearranged IgH gene as a marker appears feasible.