In recent years, DNA-arrays, gene expression profiling and next-generation sequencing have elucidated the high complexity of genomic alterations occurring in lymphoid malignancies. These studies have also contributed to the identification of new diagnostic and prognostic biomarkers, which may represent possible targets for new therapeutic approaches. Such recent advances have significantly expanded the application of molecular tests to routine diagnostic hematopathology. It is thus conceivable that next-generation assays will soon flank traditional clonality tests and chromosomal translocation assays in the diagnostic work-up of difficult cases. This review is focused on the application of molecular biology techniques in the study of lymphoid tumors. Both conventional and next-generation tests will be addressed, with particular attention to their application to clinical practice.