Lymphomas represent a heterogenous group of lymphoid neoplasms with a broad spectrum of clinical presentations and challenges in therapy resistance and relapse. Response to treatment and prognosis vary between and within lymphoma subtypes. The introduction of high-throughput molecular profiling methods and next-generation sequencing technologies has significantly enhanced our understanding of lymphomagenesis and improved the description of the tumour subtypes at the molecular level. Still, the current diagnosis of lymphomas is mostly based on morphological evaluation and immunophenotyping. This article describes how newly developed molecular assays already complement clinical diagnoses and have an impact on disease classification. Also, their contribution to risk stratification, therapy prediction, and disease monitoring for certain categories of lymphomas is discussed.