BACKGROUNDCentral nervous system involvement is a well recognized complication of systemic non‐Hodgkin lymphoma. Most central nervous system recurrences occur within the first 2 years after the initial diagnosis and are considered to represent clonally related recurrence of systemic disease. The authors attempted to investigate the clonal relation between the late‐delayed central nervous system involvement and the original systemic tumor.METHODSThe authors studied archival, formalin fixed, paraffin embedded tissue samples from 8 patients with isolated cerebral involvement diagnosed > 3 years after their initial presentation with aggressive, systemic, B‐cell non‐Hodgkin lymphoma. The rearranged immunoglobulin heavy‐chain variable region genes (VH) from both sites were amplified by polymerase chain reaction and were sequenced when necessary.RESULTSIn three of five patients who had interpretable results, a distinct, monoclonal, VH family‐specific band profile was obtained from the cerebral and systemic lymphoma. In the other two patients, a similar VH band pattern was observed and also was compared using direct sequencing, which demonstrated sequence differences between tumors from the two sites.CONCLUSIONSClonal variance between the cerebral and systemic lymphoma in these patients suggested the possibility that some instances of late‐delayed recurrence in the central nervous system represent a second, new B‐cell lymphoma rather than a true recurrence of the original systemic tumor, a finding that may have significant clinical and biologic implications. Cancer 2004. © 2004 American Cancer Society.