Background: HER2-positive/ER+ and HER2-positive/ER– breast cancers have different patterns of gene expression and intracellular pathway activation. We assessed the role of selected biomarkers in predicting the likelihood of achieving a pathological complete response (pCR) in the NeOAdjuvant Herceptin (NOAH) trial, which recruited 334 patients. Methods: Formalin-fixed paraffin-embedded core biopsies were collected from 114 women randomized to receive trastuzumab (H) with doxorubicin/paclitaxel followed by CMF (Arm CTH) or chemotherapy alone (Arm CT). Expression of the following genes and metagenes was profiled on Affymetrix 2.0 Plus: MYC, PIK3CA, PIK3R1, PTEN, amphiregulin (AREG), epiregulin, 8q24 and 8q22 amplicons, plasma cell (PC) and IGF metagenes. ER status was based on ESR1 gene expression. pCR was defined as the absence of residual invasive tumor in the breast and axillary lymph nodes. Biomarkers were assessed as continuous variables by univariate logistic regression analysis. Results: 80 samples (70%) were ER– and 34 (30%) were ER+. In the CT arm AREG (p=0.03) and 8q22 (p=0.06) were associated with lower pCR rates among ER– samples, while PTEN (p=0.01) was associated with higher pCR rates. Among ER– samples in the CTH arm, AREG (p=0.04) and IGF (p=0.007) were associated with resistance, while PC showed a trend for higher pCR rate (p=0.079). There were significant interactions between the treatment arms and 8q22 (p=0.03) and PC (p=0.04). In the high tertile of 8q22 the pCR rates were 0% (0/12 Arm CT) and 67% (10/15 Arm CTH) while for PC the pCR rates were 13% (2/15 Arm CT) and 83% (10/12 Arm CTH). There were no statistically significant associations for ER+ tumors, but a significant interaction for the likelihood of pCR and ER status was observed for PTEN (p=0.006) and PC (p=0.05) in the CT Arm and for AREG (p=0.03) in the CTH Arm. Conclusions: High expression of the PC metagene and the 8q22 amplicon, and low expression of the IGF metagene, were associated with the increased pCR rate reported with the addition of H to CT in HER2-positive/ER– tumors. The concept that HER2-positive/ER+ and HER2-positive/ER– tumors are driven by different biologic pathways warrants further investigation.