The majority of B cell lymphomas, but only a minority of T cell lymphomas, are characterized by recurring chromosome translocations. Many involve the immunoglobulin or T cell receptor loci with various partner chromosomes and lead to abnormal proto-oncogene expression. Other recurring translocations result in the production of a novel fusion protein. The detection of translocations is of particular value in diagnosis and in the detection of minimal residual disease. Aneuploidy and deletion of specific chromosome regions are common secondary chromosomal events which are rarely specific to a particular type of lymphoma but provide valuable prognostic information. Analysis by G banding, 24-colour FISH and CGH provides global genomic information; however, more specifically directed investigations utilizing locus-specific FISH probes, PCR techniques or monoclonal antibodies may be more appropriate to answer particular questions regarding diagnosis and prognosis. The known molecular consequences of abnormalities and the appropriate methods of detection are discussed for each subtype of lymphoma.