To investigate cytogenetic evolution after upfront autologous stem cell transplantation for newly diagnosed myeloma we retrospectively analyzed fluorescence in situ hybridization results of 128 patients with paired bone marrow samples at primary diagnosis and relapse. High-risk cytogenetic abnormalities (deletion 17p and/or gain1q21) occurred more frequently after relapse (odds ratio: 6.33; 95% confidence interval: 1.86,33.42;p<0.001). No significant changes were observed for defined IgH translocations (t(4;14); t(11;14); t(14;16)) or hyperdiploid karyotypes between primary diagnosis and relapse. IgH translocations with unknown partners occurred more frequently at relapse. New deletion 17p and/or gain 1q21 were associated with cytogenetic heterogeneity, since some de novo lesions with different copy numbers were present only in subclones. No distinct baseline characteristics were associated with the occurrence of new high-risk cytogenetic abnormalities after progression. Patients with relapse after novel agent-based induction therapy had an increased risk of developing high-risk aberrations (odds ratio 10.82 [1.65,127.66];p=0.03) compared to those being treated with conventional chemotherapy. Survival analysis revealed dismal outcome regardless whether high-risk aberrations were present at baseline (hazard ratio:3.53 [1.53,8.14];p=0.003) or developed at relapse only (hazard ratio 3.06 [1.09,8.59]; p=0.03). Our results demonstrate cytogenetic evolution towards high-risk disease after autologous transplantation and underline the importance of repeated genetic testing in relapsed myeloma (EudraCT number of HD4 trial: 2004-000944-26).