Thin sections of shells from different species of mollusc have been analysed by X-ray synchrotron diffraction using the BM16 at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. A sequence of 2-D X-ray diffraction patterns were acquired in transmission mode at regular intervals across the shell thickness. From the 2D patterns, 2𝛉- and χ-scans were calculated and analysed. We studied the evolution of the shell microstructures by analysing several parameters from calculated scans: (1) the intensity of the most intense aragonite reflections in the calculated 2𝛉 scans; (2) the crystallinity calculated from the full width at half maximum values of the main reflections in those scans; and (3) the degree of orientation of crystals, measured from the angular width (in angle) of the arches displayed in the Debye-Scherrer rings which appeared in the 2D diffraction patterns. The determined parameters displayed sharp changes at the transitions between microstructurally distinct shell layers indicating that the microstructural switch occurred very rapidly and was precisely controlled.