Purpose To estimate the accuracy of predicting response to neoadjuvant chemotherapy (NACT) in patients with locally advanced breast cancer using MR spectroscopy (MRS) measurements made very early in treatment. Materials and Methods This prospective Health Insurance Portability and Accountability Act (HIPAA)–compliant protocol was approved by the American College of Radiology and local‐site institutional review boards. One hundred nineteen women with invasive breast cancer of ≥3 cm undergoing NACT were enrolled between September 2007 and April 2010. MRS measurements of the concentration of choline‐containing compounds (tCho) were performed before the first chemotherapy regimen (time point 1, TP1) and 20–96 h after the first cycle of treatment (TP2). The change in tCho was assessed for its ability to predict pathologic complete response (pCR) and radiologic response using the area under the receiver operating characteristic curve (AUC) and logistic regression models. Results Of the 119 subjects enrolled, only 29 cases (24%) with eight pCRs provided usable data for the primary analysis. Technical challenges in acquiring quantitative MRS data in a multi‐site trial setting limited the capture of usable data. In this limited data set, the decrease in tCho from TP1 to TP2 had poor ability to predict either pCR (AUC = 0.53, 95% confidence interval CI: 0.27–0.79) or radiologic response (AUC = 0.51, 95% CI: 0.27–0.75). Conclusion The technical difficulty of acquiring quantitative MRS data in a multi‐site clinical trial setting led to a low yield of analyzable data, which was insufficient to accurately measure the ability of early MRS measurements to predict response to NACT. Level of Evidence: 1 Technical Efficacy: Stage 2 J. MAGN. RESON. IMAGING 2017;46:290–302