Primary large-cell anaplastic lymphomas (LCAL) presenting in the gastrointestinal tract are rare and sometimes difficult to distinguish from nonlymphoid tumors. Because recognition of these tumors as lymphoma has clinical and prognostic implications for the patient, the diagnostic contribution of genotyping by polymerase chain reaction (PCR) and of immunophenotyping was evaluated in 16 routinely processed samples of gastric and small-intestinal LCALs. Gene rearrangement analysis was done with primers for the immunoglobulin heavy (IgH) and T-cell receptor gamma(TCR gamma) chain. Nine of the 16 cases were assigned to T- or B-lymphoid lineage immunophenotypically. Twelve of the 16 samples had a predominant T- or B-cell clone by PCR. Combination of both methods resulted in lineage assignment of 14 cases (9 T-LCAL, 5 B-LCAL). Two LCAL samples were EBV positive by PCR, one also by immunophenotyping. High expression levels of p53 did not correlate with the presence of EBV or cell lineage. Thus, gene rearrangement studies on routinely processed biopsy specimens by PCR are practical and add to the diagnostic repertoire in cases of gastrointestinal large-cell tumors of immunophenotypically undefined lineage.