Background: Genomic instability (GI) drives tumor development, generates selective clonal competence and enhances cancer aggressiveness. Copy Number Alterations (CNAs) data from a cohort of pre- and post-treatment (ttm) breast cancer (BC) tumors from patients (pts) in neoadjuvant trials GEICAM/2006-03 (NCT00432172) and GEICAM/2006-14 (NCT00841828) were used to obtain a GI Index for each sample. We analyzed the variation of GI index induced by therapy and their associations with tumor phenotype. Methods: GEICAM/2006-03 HER2-negative pts were selectively treated according to clinical subtypes: triple negative (TN) pts were treated with standard taxane/anthracycline-based chemotherapy (TA-CT) +/- carboplatin, while luminal patients were randomized to TA-CT vs. hormonotherapy; GEICAM/2006-14 HER2+ pts received TA-CT plus anti-HER2 therapy. Shallow-whole genome Illumina sequencing DNA data from 204 paraffin-BC (100 pre- and 104 post-ttm tumors) were segmented to obtain CNAs. The area under the segmentation curve (sum of segmented mean normalized by CNAs number) was calculated for each sample as index of GI. Differences between GI indexes in pre- and post-ttm samples were analyzed using Wilcoxon test. Results: A significant reduction in GI index was observed after ttm compared to pre-therapy samples (p = 5.1e-07), which was confirmed in a subset of pre/post-therapy paired tumors (N = 39, p = 0.0034). Luminal (61%) tumors revealed a significant decrease in GI index, both in overall population (median GI index: 0.141 pre-ttm vs 0.068 post-ttm, p = 1e-09) and in paired samples (0.126 vs 0.072, p = 0.00013). Similarly, HER2+ (9%) tumors showed a trend towards GI reduction (0.143 vs 0.079, p = 0.085). In contrast, TN (30%) cases presented an increasing trend in GI index in the residual tumor (0.132 pre- vs 0.17 post-ttm, p = 0.68). Conclusions: Our data suggest that GI could be a direct target of neoadjuvant therapy in BC. Treatment seems selectively eliminate tumor cells with higher genomic aberrations in luminal and HER2+ BC, resulting in a reduction of GI index in the residuals tumors. In contrast, according to previous publications, we suggest that GI could be a mechanism of adaptative CT resistance in TNBC. Clinical trial information: GEICAM/2006-03 NCT00432172. GEICAM/2006-14 NCT00841828.