Bone marrow biopsies (BMB) are the conventional staging method for assessing marrow involvement by lymphoma. Morphological criteria provide basic data determining their dignity, but concerning microfocal infiltrates, these criteria are rather inaccurate. Here, by examination of immunoglobulin H (IgH) receptor rearrangement and comparison of medullar and nodular lymphoma sites, diagnostic reliability was improved. Employing non-nested IgH rearrangement analysis with FR3A and JHa consensus primers, B-cell clonality was assessed on glutardialdehyde fixed, decalcified BMB with and without lymphoma infiltration and on the corresponding lymph node specimens. Malignancy was confirmed when polymerase chain reaction (PCR) generated no more than two peaks and was observed in 60% of the medullar B-cell lymphoma. Comparison of lymph node tissues and BMB revealed an identical pattern in 50% of the probes. In 25% of the cases a single clonal peak derived from the lymph node tissues was also observed in the BMB but was surrounded by additional peaks. Here, direct comparison of the data permitted determination of lymphoma in the BMB. Therefore, IgH FR3 PCR analysis is a suitable tool to examine small lymphoid infiltrates in BMB, and direct comparison with corresponding nodal lymphoma can further facilitate estimation of their dignity.