: A new method for infrared analysis of tissues and cells is presented. The method is based on Fourier transform infrared microspectroscopy coupled with attenuated total reflectance. The technique allows spectroscopic measurements on the same samples used by pathologists for histopathological evaluation, e.g. stained samples on plain glass slides. Since the same specimen can be used as for histopathology, the method does not require sample preparation or modification. Significantly, the sample is not damaged. Glass absorbs in the infrared and thus has not been used previously in infrared analysis of tissues and cells. Conventional infrared techniques utilize expensive substrates, such as BaF2 windows and gold coated slides which do not absorb infrared radiation. However, these measurements require special preparation and result in the destruction of the sample. Breast cancer tissues were examined to demonstrate the feasibility and reproducibility of the new method. Linear discriminant analysis was used to discriminate and classify three types of cells: benign, atypical hyperplasia and malignant. It was demonstrated that benign vs. malignant cells were discriminated with 100% accuracy, benign vs. atypical hyperplasia were discriminated with 100% accuracy and malignant vs. atypical hyperplasia were discriminated with an accuracy of 90% and higher.