An extremely rare case of primary non-Hodgkin’s lymphoma of the larynx (Stage IE) diagnosed by gene rearrangement is reported. The patient was a 76-year-old man with a chief complaint of pharyngeal discomfort. Remission was obtained by excision of the tumour and radiotherapy. Surface phenotypic studies of the laryngeal lesion demonstrated a main population of B-cells expressing L-26, some of the atypical lymphocytes positive with UCHL-1. Genotypic analysis of the specimen disclosed a clonal rearrangement of the immunoglobulin heavy chain with the same rearrangement pattern. These data indicate that this patient had non-Hodgkin’s lymphoma with diffuse large B-cell type. Gene rearrangement analysis was useful for diagnosis. Diagnostic and therapeutic options are discussed in light of the current literature.