Clonal karyotypic abnormalities characteristic of myelodysplastic syndrome (MDS) occur in up to 18% of patients who undergo autologous bone marrow transplantation (auto-BMT) for the treatment of lymphoma. Morphologic changes are often subtle and may not meet the French-American-British Cooperative Group criteria for MDS. We retrospectively assessed dysplastic changes in peripheral blood and bone marrow specimens obtained before and after transplantation from nine patients and correlated them with karyotype and survival. All patients had normal cytogenetic study results before transplantation and had clonal karyotypic abnormalities develop after auto-BMT. Four patients (with aggressive MDS) survived a short time and died of acute myelogenous leukemia or MDS-related complications, four (with indolent MDS) had a prolonged survival period, and one patient died of recurrent lymphoma. The group with aggressive MDS had significantly more bone marrow trilineage dysplasia before auto-BMT than did the group with indolent MDS or cytogenetically normal auto-BMT controls, suggesting that stem cell damage occurred before transplantation and was not detected by pretransplantation cytogenetic analysis. Comparatively greater dyserythropoiesis and dysmegakaryopoiesis were present after transplantation; these changes were similar to those seen in de novo MDS. Posttransplantation dysplasia in the group with indolent MDS was analogous to the atypia related to the transplantation process.