The hair cuticle provides significant protection from external sources, as well as giving rise to many of its bulk properties, e.g., friction, shine, etc. that are important in many industries. In this work, atomic force microscopy-infrared spectroscopy (AFM-IR) has been used to investigate the nanometer-scale topography and chemical structure of human hair cuticles in two spectral regions. AFM-IR combines atomic force microscopy with a tunable infrared laser and circumvents the diffraction limit that has impaired traditional infrared spectroscopy, facilitating surface-selective spectroscopy at ultra-spatial resolution. This high resolution was exploited to probe the protein secondary structures and lipid content, as well as specific amino acid residues, e.g., cystine, within individual cuticle cells. Characterization across the top of individual cells showed large inhomogeneity in protein and lipid contributions that suggested significant changes to physical properties on approaching the hair edge. Additionally, the exposed layered sub-structure of individual cuticle cells allowed their chemical compositions to be assessed. The variation of protein, lipid, and cystine composition in the observed layers, as well as the measured dimensions of each, correspond closely to that of the epicuticle, A-layer, exocuticle, and endocuticle layers of the cuticle cell sub-structure, confirming previous findings, and demonstrate the potential of AFM-IR for nanoscale chemical characterization within biological substrates.