This article deals with the structure of the cell membrane complex (CMC) in the human hair cuticle. The microbeam X-ray provided a pattern of small-angle scattering from the CMC in the cuticle with no sample preparations, including slicing and pre-staining of hair. The thickness of the beta- and delta-layers, substructure in CMC, was estimated by analysis of the scattering pattern. We used hair samples extracted with several solvents, and found that solvent extraction changed the thickness of the beta- and delta-layers in a manner dependent on the type of solvent. Extraction of hair with solvent was also shown to have effects on the extent of dyeing. There was a high correlation between the extent of dyeing and the thickness of the delta-layer, i.e., a thin layer tended to show a high amount of dyeing, whereas there was no significant correlation between the thickness of the beta-layer and the extent of dyeing.