This study quantitatively evaluated intra-tumoral heterogeneity through histogram analysis of synthetic MRI parameters, and determined correlations with prognostic factors and molecular subtypes of breast IDC. We found that IDC with high nuclear grade had higher PD10th, PDmean, PDmedian and PDmax. PDmedian was higher in IDC with HER2 positivity. T110th was higher in cancers with PR negativity. Cancers with hormone receptornegativity had higher T210th, T2mean and T2median than that with hormone receptor positivity. Overall, we demonstrated that whole-tumor histogram-based imaging features derived from synthetic MRI correlated with prognostic factors and may be considered a non-invasive approach for discriminating IDC subtypes.