Tooth enamel, the outermost layer of human teeth, is a complex, hierarchically structured biocomposite. The details of this structure are important in multiple human health contexts, from understanding the progression of dental caries (tooth decay) to understanding the process of amelogenesis and related developmental defects. Enamel is composed primarily of long, nanoscale crystallites of hydroxyapatite that are bundled by the thousands to form micron-scale rods. Studies with transmission electron microscopy show the relationships between small groups of crystallites and X-ray diffraction characterize averages over many rods, but the direct measurement of variations in local crystallographic structure across and between enamel rods has been missing. Here, we describe a synchrotron X-ray-based experimental approach and a novel analysis method developed to address this gap in knowledge. A 500-nm-wide beam of monochromatic X-rays in conjunction with a sample section only 1 μm in thickness enables 2D diffraction patterns to be collected from small well-separated volumes within the enamel microstructure but still probes enough crystallites (300 per pattern) to extract population-level statistics on crystallographic features like lattice parameter, crystallite size, and orientation distributions. Furthermore, the development of a quantitative metric to characterize relative order and disorder based on the azimuthal autocorrelation of diffracted intensity enables these crystallographic measurements to be correlated with their location within the enamel microstructure (e.g., between rod and interrod regions). These methods represent a step forward in the characterization of human enamel and will elucidate the variation of the crystallographic structure across and between enamel rods for the first time.