Attenuated total reflection Fourier transform infrared (ATR–FT-IR) spectroscopy of hair fibres shows a discrete transition zone (DTZ) between the hard protective cuticle layer and the softer elongated cortical cells of the cortex. The DTZ is composed of flattened orthocortical cells located on the outer perimeter of the cortex and appears to range in thickness between 2 and 3.6 μm. The inner surface of the DTZ, adjacent to the elongated cortical cells that make up the core of the hair fibre, is irregular. ATR–FT-IR analyses of these flattened orthocortical cells indicate major changes in the molecular structure of keratins found in this transition zone. Other studies have identified cells that produce keratins that are distinct from alpha keratins found in the elongated heterocortical cells in the hair fibre core. These distinct keratins appear to be produced in the lower region of the hair follicle at the interface between the cuticle and cortex.

The DTZ is also the region where ATR–FT-IR spectroscopy studies identified changes in C−H bending of lipid esters indicative of breast cancer. Lipid ester absorption bands at 1738 and 1732 cm−1, present in non-cancer hair, are absent in the cancer hair and a new ester band absorbing at 1736 cm−1 is observed. When the breast cancer is clinically removed, the 1736 cm−1 ester band absorption and the increase in the 1446–1456 C−H-bending absorption ratio are no longer observed. This suggests that biomarkers produced by the breast cancer interact with stem or other cells near the lower region of the follicle, controlling the amount and type of lipid esters in the DTZ.