Abstract Background: Type II microcalcifications, most often seen in proliferative lesions, including both benign and malignant pathologies. But whether the emergence of type II microcalcifications associated with cell canceration is still not clear now. Raman spectroscopy is a powerful, non-invasive analytical tool which can provide detailed and meaningful information about biochemical composition of tissues at molecular level. Our aim was to find the differences and relationships of type II microcalcifications between fibroadenoma, ADH tissues, and DCIS, IDC in breast based on their various biochemical characteristics by Raman spectroscopy. Methods: The frozen sections were collected from 15 patients (all female; ages 25-57) who underwent surgical resection or mammotome biopsy at the Department of Breast Surgery, the First Hospital of Jilin University. After operation the samples were immediately frozen at -20∼-25° and two contiguous sections (6 µm thickness) were cut from a sample by freezing microtome. One was stained with haematoxylin and eosin for routine histopathological analysis and found the microcalcification locations by three expert breast pathologists; the same position of the other section was detected by Microscopic confocal Raman spectrometer (HORIBA JY Lab800, 633nm) with its mirror image (the H&E section). After the spectra we needed had been obtained, the Au@SiO2 shell-isolated nanoparticles (SHINs) were added to the surface of frozen sections immediately and then the spectra with SHINs were collected. Results: A total of 122 Raman spectra and 119 SHINERS spectra were obtained from the microcalcifications in 3 fibroadenoma tissues, 3 ADH, and 5 DCIS, 4 IDC breast tissues. The Raman signals were significantly enhanced by SHINs. Except the major peak at 958-960 cm-1 which attributed to the vibrational modes of calcium hydroxyapatite, the results show no calcium oxalate dihydrate peaks but several other chemical species. The peaks of these species appear at 1002, 1072, 1126, 1446, 1556, and 1657 cm-1, these are attributed to amino acid residue (phenylalanine), nucleic acids, lipids, carotenoids, and Amide I, respectively. The fibroadenoma and ADH microcalcifications mean spectral have the same peak at 1072cm-1, which belongs to the O-P-O stretch of nucleic acids, but in DCIS and IDC tissues the peak changes to 1078cm-1. The ADH have more obvious peak at 1657 cm-1 which assigned to different vibrational modes of the backbone and Amide I, but in DCIS and IDC tissues, the Amide I bands were disappeared. In the DCIS microcalcifications mean spectral, the peaks attributed to amino acid residue (phenylalanine) at 1003, 1031 cm-1 and lipids (CH2 and CH3 bending) at 1301, 1441 cm-1 show more stronger. Meanwhile, compare with DCIS, the IDC spectral shows more stronger nucleic acids peaks and weaker lipids peaks. Conclusion: We have demonstrated the potential of SHINERS to differentiate Type II microcalcifications found in fibroadenoma, ADH, and DCIS, IDC breast tissues. The results presented in this paper provide the biochemical characteristics of the Type II microcalcifications among these tissues, and may represent a key factor responsible for mechanisms of carcinogenesis. Citation Format: Haipeng Zhang, Bing Han, Chao Zheng, Ye Du, Lijia Liang, Weiqing Xu, Zhimin Fan. Exploring type II microcalcifications in benign, premalignant and malignant breast lesions by shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-05-15.