In bone marrow trephines, morphological and immunohistochemical criteria may not be sufficient to discriminate reactive from malignant lymphoid infiltrates. The aim of this study was to determine whether the detection of clonal immunoglobulin heavy chain (IGH) gene rearrangements is a reliable and specific marker for malignant B-cell clones in bone marrow biopsies. Bone marrow trephines with infiltration by different types of low-grade B-cell non-Hodgkin lymphoma (n = 32), reactive lymphoid hyperplasia (n = 18), and reactive lymphoid aggregates (n = 15), including 5 patients with rheumatoid or other autoimmune disorders, were analyzed by morphology, immunohistochemistry, IGH gene rearrangement (polymerase chain reaction), and DNA sequence analysis in selected cases. In 22 (68.8%) of 32 patients with B-cell non-Hodgkin lymphoma, a clonal IGH gene rearrangement was detected. Of the reactive cases, 1 of 18 patients with lymphoid hyperplasia demonstrated clonality, and 9 (60%) of 15 patients with reactive lymphoid aggregates gave a clonal result (GeneScan analysis). DNA sequence analysis was performed in 7 of the latter patients confirming clonality in 6. Four of the patients with B-cell clonality had an autoimmune disorder. None of these patients developed a malignant lymphoma during follow-up. Thus, the molecular detection of a clonal rearrangement of the IGH gene may support the diagnosis of a malignant lymphoma infiltrating the bone marrow. However, morphologically and immunohistochemically benign lymphoid aggregates might also harbor B-cell clones especially in patients with autoimmune disorders. Therefore, the detection of clonality has to be interpreted with utmost care and does not qualify for the unequivocal diagnosis of a malignant B-cell lymphoma.