The polymerase chain reaction (PCR) offers a practical means of studying the molecular genetic features of lymphomas. The method is rapid and, as formalin-fixed, paraffin processed samples can be used, does not require special tissue handling procedures. PCR amplified immunoglobulin and T cell receptor gene rearrangements can be exploited as markers of clonality and lineage and genetic abnormalities such as chromosome translocations and mutations of oncogenes and tumour suppressor genes can be used to identify specific lymphoma types. Polymorphic X linked loci may also be used as markers of clonality in females. Direct sequencing of PCR amplified IGH variable regions has provided insights into the developmental stages, susceptibility to antigen drive and dissemination patterns of lymphomas. The role of oncogenes and tumour suppressor genes such as MYC and TP53 in lymphomas can be studied by PCR amplification of mutation hotspots and direct sequencing of products. Known viral and bacterial DNA can readily be identified using PCR and unknown organisms sought using conserved primers to amplify polymorphic sequences. PCR analysis of the lymphomas and related disorders has accelerated our understanding of their molecular biology and provides a practical tool with diagnostic and prognostic applications. Future development of in situ PCR methods will provide cellular localization of genetic defects and infectious agents.