We propose a new method of investigating variation of preservation within a parchment sample, which allows a more detailed analysis of alteration of the material structure. X-ray diffraction analysis of parchment typically involves the sample aligned with the plane of the parchment perpendicular to the direction of the X-ray beam, with a beam size of approximately 200 mum and an image consisting of the composite diffraction features from the entire thickness of the sample. Here we describe the use of microfocus X-ray beams, with a beam size of 1.5 mum vertically x 15 mum horizontally, to carry out surface-to-surface scans of thin sections of parchment. Up to 200 images can be taken in a single cross-sectional scan of a 300 mum thick parchment section. This allows for X-ray diffraction analysis of features present only in specific areas of the parchment, such as at the surface. The orientation of collagen fibrils in the plane of the parchment, the effects of laser cleaning (including possible laser induced damage), mineral phases and crystalline lipids present in samples, and parchment structure under an inked region are investigated. It is shown that the long collagen fibril axis lies parallel to the parchment surface throughout the sections. Laser cleaning appears not to damage the collagen in parchment, while laser-damaged samples display gelatinization of the collagen at the surface. Polymorphs of calcium carbonate were detected in several samples but in most cases were not confined to the surfaces, as would be expected if the chalk finishing process was the main source of mineral phases in parchment. Crystalline lipid is found in most samples and appears to exhibit a preferential alignment with the plane of the phospholipid bilayer arranged parallel to the long fibril axis of collagen. The d spacing of the lipid is variable throughout a parchment section, indicating fluctuations in the hydration state, phase, or biochemical composition of the lipid. Ink affects the parchment to a depth of approximately 90 mum, as measured by principal components analysis, disrupting the structure of the collagen to this depth. These features demonstrate the ability of this technique to examine diagenesis of individual components of parchment on a scale not previously studied.