Background Topoisomerase IIa (topo IIa) protein expression has prognostic significance in many cancers. However, it is still unclear whether topo IIa protein expression and gene alterations play roles as prognostic factors in diffuse large B-cell lymphoma (DLBCL). Materials and methods We selected 102 patients with DLBCL who were homogeneously treated with CHOP chemotherapy and followed up. Using tissue microarray technology, all of the cases, consisting of 25 germinal centre B-cell-like (GCB) and 77 nongerminal centre B-cell-like (non-GCB) types, were studied. Topo IIa protein expression was detected by immunohistochemistry. Gene copy number of topo IIa was analysed by chromogenic in situ hybridization. Cox regression, chi-square test and KaplanMeier statistics were performed using SPSS 15.0. Results Topo IIa protein overexpression was found (i)n 91 (91/102, 89.2%) cases, while topo IIa gene amplification was absent in all cases. Chromosome 17 deletion was identified in 3 (3/102, 2.9%) cases, diploid in 66 (66/102, 64.7%) cases and aneuploidy in 33 (33/102, 32.4%) cases. By multivariate analysis, no significant differences in progression-free survival (PFS) and overall survival (OS) were observed in patients with topo IIa protein overexpression (P > 0.05), while chromosome 17 aneuploidy predicted worse PFS and OS (P < 0.001). Conclusions These results suggested that chromosome 17 aneuploidy, but not topo IIa protein expression, could predict worse survival in patients with DLBCL.