Inexpensive near-infrared microscopy (NIRM) was developed as a convenient technique to detect the medulla loss of scalp hair while reducing analytical time with easy sample preparation, leading to a field screening tool for breast cancer. NIRM has been evaluated as an alternative to synchrotron-based nanoscopy and to the relatively expensive method of conventional infrared microscopy to determine the degree and pattern of medulla loss of scalp hairs of patients with breast cancer and benign diseases, as well as normal healthy individuals. NIR imaging showed a strong, scattering-based hyperintense contrast of the medulla compared to the fully attenuated cortex in medullated healthy hair. Complete medulla loss (CML) per hair strand was more extensively (60.9  ±  10.2  %  ) (p  <  0.001) detected in the hair of all cancer patients than in the hair of either healthy individuals (less than 3.7  ±  7.5  %  ) or those with benign disease (30.6  ±  5.9  %  ), suggesting a potential biomarker for breast cancer diagnosis. The medulla structure was retained mostly in the hair of age-matched healthy individuals, but discontinuous medulla loss was observed concomitantly with less CML in fibroadenoma patients. Potentially, compact NIRM modules can be integrated into a mobile platform as point-of-care technology for breast cancer screening.