Variations in hair shaft morphology reflect ethnical diversity, but may also indicate internal diseases, nutritional deficiency, or hair and scalp disorders. The measurement and the follow-up of the hair shaft thickness over a defined period of time would be a valuable diagnostic tool in clinical practice. Standard light microscopy (LM) measurements require the epilation of hair shafts and frequently yield inaccurate values caused by the elliptic geometry of human hair shafts. Optical coherence tomography (OCT) is a noninvasive investigation method based on the principles of Michelson interferometry with a detection depth of approximately 1 mm in human skin. Two-dimensional images of the cross sections of tissue samples at a resolution of approximately 10 μm are produced, which allows convenient calculation of hair shaft thickness. To evaluate this new methodology for hair shaft thickness measurements, hair shafts taken from 28 healthy volunteers were analyzed by in vivo OCT and compared to standard in vitro LM measurements of hair shaft thickness. OCT yielded highly reproducible measurements of hair shaft thickness with a distinctly reduced variation compared to standard LM. This technique offers a unique opportunity for in vivo measurement and a follow-up of the kinetics of hair shaft thickness in humans during medical therapy.