The prognostic value and the best method of testing of topoisomerase II alpha (TOP2A) status have not been established in modern tailored therapy based on breast cancer subtype. The frequencies of TOP2A overexpression and amplified were 55.8% and 9.5%, respectively. TOP2A overexpression correlated strongly with non-luminal A subtype (χ -test, 0.001). TOP2A overexpression was significantly associated with relapse-free survival in luminal B breast cancer ( = 316; log rank test, 0.001) but not in other breast cancer subtypes. Cox regression analysis showed that TOP2A overexpression is a significant prognostic factor in luminal B breast cancer (hazard ratio (HR) 4.00, 95% confidence interval (CI) 1.65-9.54, = 0.002). amplified was recognized in HER2 positive breast cancer ( 0.001). In HER2 positive breast cancer, amplified (HR 0.30, 95% CI 0.085-1.07, = 0.063) appeared to be a better prognostic factor. In modern tailored therapy, TOP2A overexpression can be a poor prognostic factor in luminal B breast cancer. In contrast, amplified could be a better prognostic factor in HER2 positive breast cancer. Between May 2005 and April 2015, a total of 643 consecutive non-metastatic invasive breast cancers were evaluated for amplified using fluorescence hybridization analysis (FISH) and for TOP2A overexpression using the immunohistochemistry assay. FISH ratios of 2 or higher were designated as amplified, and TOP2A staining >10% was defined as TOP2A overexpression. The prognostic values of amplified and TOP2A overexpression were retrospectively evaluated.