We studied the flow cytometric immunophenotyping (FCI) and genotypic data of 11 specimens from 10 transplant recipients and categorized them based on a scheme for posttransplant lymphoproliferative disorders (PTLDs). Specimens had been analyzed by polymerase chain reaction and/or Southern blot for T-cell and B-cell (immunoglobulin heavy chain and light chain genes) gene rearrangements (BGR). The categories for PTLDs were as follows: 1, 1; 2, 6; and 3, 4. The plasmacytic and polymorphic B-cell hyperplasias (PBCHs) revealed no monoclonal/aberrant cells by FCI or genotypic studies (GS). Three of 4 polymorphic B-cell lymphomas (PBCLs) revealed monoclonal or aberrant (no surface light chain) B cells by FCI; 1 of 3 revealed a BGR. However, the 1 case with no monoclonal/aberrant B cells by FCI revealed a BGR. Both immunoblastic lymphomas revealed monoclonal or aberrant B cells by FCI; 1 revealed a BGR. Both multiple myelomas revealed monoclonal plasma cells by FCI; 1 revealed a BGR. In the 4 PTLDs with monoclonal/aberrant B cells by FCI and no clonality detected by GS, the GS were performed on fresh and paraffin-embedded tissue samples. FCI of the plasmacytic and PBCHs supported no clonal process by GS. FCI defined a clonal process in 2 PBCLs, I immunoblastic lymphoma, and 1 multiple myeloma that were negative by GS. However, 1 PBCL that was polyclonal by FCI was monoclonal by GS. Thus, FCI is useful for identifying a clonal process in PTLDs with negative results by GS; FCI and GS should be performed routinely in PTLDs to detect a clonal process.