Multiple myeloma (MM) is a neoplasm characterized by proliferation of clonal plasma cells (PCs) and a combination of clinical manifestations. Flow cytometry is an important method for diagnosing and monitoring of MM. Cytogenetic profiling of neoplastic PCs provides important prognostic information. Although stem cell transplantation (SCT) has significantly improved the overall survival of patients with MM, most SCT recipients relapse. We have studied the immunophenotypic and cytogenetic dissimilarities in the neoplastic PCs before SCTand after relapse in patients with initial complete remission, and investigated a possible influence of such dissimilarities on the patients' survival. We retrospectively reviewed results of flow cytometric studies of bone marrow specimens from 46 patients with MM who underwent SCT, demonstrated a complete initial response, but subsequently relapsed. In nine of these patients, fluorescence in situ hybridization (FISH) studies were performed both pre-SCTand post-relapse. We have shown a significant flow cytometric and cytogenetic diversity of the neoplastic PCs in relapsed MM post-SCT. Such changes were detected in a considerable number of cases (47.8% and 44.4%, respectively). The most frequent cytogenetic changes indicate an emergence of possibly a more aggressive PC clone, known to be associated with worse prognosis and poorer outcome. Our study has demonstrated that the acquisition of immunophenotypic changes predicts worse overall survival. Keywords Multiple myeloma. Flow cytometry. Karyotype. Relapse. Stem cell transplant Reha M. Toydemir and Anton V. Rets contributed equally to this work.