Twelve cases of large granular lymphocytosis were examined by flow cytometry and Southern blot analysis to correlate immunophenotypic and molecular genetic markers with clinical features. Nine cases fulfilled clinical criteria for the lymphoproliferative disorder of granular lymphocytes, and eight of these demonstrated the molecular features of T-cell-type lymphoproliferative disorder of granular lymphocytes including surface expression of CD3, expression of one or more natural killer (NK)-cell antigens (CD11b, CD16, or CD57), and clonal rearrangement of both the T-cell receptor beta- and gamma-chain-joining genes. One of these cases demonstrated coexisting clonal rearrangement of the immunoglobulin heavy-chain-joining genes, but none demonstrated kappa-light-chain-joining gene rearrangement. The eight T-cell lymphoproliferative disorder of granular lymphocytes cases all lacked expression of the NK antigen CD56 (NKH1). In contrast, the other case of lymphoproliferative disorder of granular lymphocytes rapidly evolved into an aggressive NK-cell lymphoma which did not express CD3, did express CD56, had germline T-cell receptor gene configurations, and had multiple clonal chromosomal abnormalities. This case demonstrated nasal cavity and cutaneous tumor infiltrates consistent with previously described CD3-negative, CD56-positive NK-cell lymphoma of the upper aerodigestive tract. Three cases of transient large granular lymphocytosis demonstrated germline T-cell receptor gene configurations. This study demonstrates the usefulness of Southern blot analysis and flow cytometry in characterizing proliferations of large granular lymphocytes. The transformation of a single case into an aggressive NK-cell lymphoma with blastic morphology and tissue infiltration was associated with a fatal outcome.