Mature B- and T-cell lymphomas are increasingly being associated with specific genetic alterations; characterization of these changes can sometimes be crucial to both diagnosis and prognosis. Molecular testing encompasses florescence in situ hybridization (FISH) and polymerase chain reaction (PCR)-based assays, as well as classical cytogenetics. FISH and PCR-based assays can be performed on cytology material without the need for advanced planning for testing with fresh tissue. As many lymphoproliferations are amenable to fine needle aspiration diagnosis, it is important for the cytopathologist to be aware of what testing is feasible in these (sometimes limited) specimens. Here, we review pertinent genetic changes in mature B- and T-cell lymphomas with a focus on those that may be encountered more commonly in cytology specimens. Diagn. Cytopathol. 2012;40:542–555. © 2012 Wiley Periodicals, Inc.