OBJECTIVE: To investigate associations between breast cancer molecular subtype and intravoxel incoherent motion imaging (IVIM) and amide proton transfer-weighted (APTw). METHODS: This prospective study involved 264 patients with suspected breast tumors who underwent both breast APTw and IVIM MRI. The maximum diameter of the tumor (Dmax), APT value, apparent diffusion coefficient (ADC), diffusion coefficient (D), pseudo diffusion coefficient (D*), and perfusion fraction (f) values along with histological subtype, grade, and prognostic factors (Ki-67, estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER-2), were compared. APT values about biological subtypes, Ki-67 labeling index, and nuclear grades (NGs) were further analyzed. RESULTS: A total of 205 participants (mean age, 53 years, range 29-80) were included in the evaluation. The triple-negative breast cancer (TNBC) cancers showed significantly higher D* values than the Luminal B cancers (P = 0.002), while there was no difference in Dmax, ADC, D, and APT (P = 0.068,0.318,0.432,0.089). The TN-type cancers showed significantly higher APT values than the HER2-type cancers (P = 0.002). The area under the curve (AUC) obtained from APTw, IVIM, and Dmax was 0.874. The APT had a moderate positive correlation with the unclear grade (r = 0.473, P <
0.001), and the D* had a weak positive correlation with the Ki-67 labeling index(r = 0.160, P = 0.022). CONCLUSION: The TN subtype of breast cancer is associated with APT value and D* from IVIM. The APTw may be a promising method for predicting TNBC molecular subtypes.