Background Cytogenetic abnormalities in multiple myeloma (MM) are one of the most important independent prognostic factors. Based on cytogenetic findings MM patients (pts.) could be divided into prognostic groups.The aim of this study was to determine the correlation between the aberration of the chromosome 13, rearrangement of IGH gene, translocations t(11;14) and t(4;14), the deletion of 17p13 and the prognostic factors in the patients with newly diagnosed MM who underwent autologous transplantation (AT) according protocol of CMG 2002 trial. Methods Fluorescence in situ hybridization and cytoplasm immunoglobulin staining (cIg-FISH) were used to detect monotypic plasma cells and aberrations mentioned above. Cytogenetic abnormalities were found in 68 newly diagnosed patients with MM, median of follow-up 35 months, median age 57 years (39-67), DS stadium: stage I 5.9%, II 25%, III 69.1%; A/B - 83.8%/16.2%. Results Overall response (OR) rate after AT was 85.3% including 20.6% CR, 30.9% VGPR and 33.8% PR. Median of time to progression (TTP) was 25.6 (0.4-41.4) months. Median of overall survival (OS) was not reached (0.4-48.5) months. The aberration of the chromosome 13 was found in 53% (35/66), IGH rearrangements in 56% (36/64), t(11;14) in 18.5% (12/64), t(4;14) in 23% (15/64) and deletion of 17p13 in 15.5% (8/51) pts. We have correlated standard prognostic factors (MIG, LD, B2M, Hb, CRP, Ca, albumin), TTP, progression free survival (PFS), duration of response (DOR) and OS with the occurrence of the mentioned aberrations. Lower albumin and lower LD concentrations were detected in patients with aberration of chromosome 13. We have observed shorter OSin patients with IGH rearrangements and then in pts without this change (p=0,029). We have found no significant difference when compared incidence of other chromosomal aberration for TTP, DOR, PFS and OS. Summary/Conclusion We have analysed data of the homogenous group of patients undergoing autologous transplantation in the CMG trial of Czech Myeloma Group. Based on the results we conclude that patients with deletion of 13q14 have lower albumin and lower LD concentration.