A patient with follicular small cleaved lymphoma presented with an unusual clinical relapse in the central nervous system (CNS) without morphologic evidence of lymphoma cells in the cerebral spinal fluid (CSF). Molecular genetic analysis of the small number of cells in the CSF after in vitro DNA amplification by the polymerase chain reaction demonstrated the presence of an abnormal translocation sequence between chromosomes 14 and 18. A similar translocation could be detected from the original fixed archival lymph node biopsy and from a small proportion of circulating mononuclear cells. These results indicated that occult lymphoma cells were present in the CSF and peripheral blood. Secondary CNS lymphoma involvement was identified at autopsy. This case demonstrates the enhanced sensitivity of lymphoma diagnosis from poorly cellular specimens after in vitro DNA amplification.