Development of a second lymphoma after autotransplantation is an unusual event. Its real incidence, however, could be underestimated, since histologic and immunophenotyping techniques are often unable to distinguish it from a relapse. We report a lymphoma patient in apparent relapse after 42 months of molecular remission achieved by autotransplantation. Sequencing analysis of the immunoglobulin heavy-chain genes showed that the rearrangement of variable, diversity and joining segments had changed between diagnosis and relapse and suggested that a second lymphoma had developed.