The purpose of this article is to determine whether the peak integral and signal-to-noise ratio (SNR) of total choline-containing compounds obtained by MR spectroscopy (MRS) correlate with histologic biomarkers currently used for predicting prognosis in patients with breast cancer. Single-voxel proton MRS using a 1.5-T scanner was performed in 184 patients (mean age, 48 years; range, 28-72 years) with breast cancer. We obtained absolute total choline-containing compound peak integral, total choline-containing compound peak integral normalized for the volume of interest, and SNR after MRI. On surgical pathology, pathologic subtype and prognostic factors such as nuclear grade, histologic grade, estrogen receptor (ER), HER-2≠neu, extensive intraductal component (EIC), lymphovascular invasion, and lymph node metastasis were also evaluated. Statistical analysis was performed using Mann-Whitney U test and Spearman rank correlation. The total choline-containing compound SNR, absolute total choline-containing compound peak integral, and normalized total choline-containing compound integral were significantly higher for invasive ductal carcinoma, cancer of high nuclear or histologic grade, and EIC-negative cancer (p < 0.001) than for in situ or other invasive carcinomas (p = 0.005), cancer of low nuclear or histologic grade (p = 0.009), and EIC-positive cancer (p = 0.017). There was a significant difference in the total choline-containing compound SNR between ER-positive and -negative groups (p = 0.007) and between triple-negative and non-triple-negative groups (p = 0.002). A positive correlation was found between the volume of interest (p < 0.001), tumor size (p = 0.011), and three MRS parameters (p = 0.003). Our study suggests that proton MRS can play a role in predicting prognostic indicators of tumor aggressiveness in patients with newly diagnosed breast cancer.