In this work, planar variation in the form of polytypes, twins, and disorder in xanthine were characterised using multi-dimensional electron diffraction modalities. By comparing relative inter-layer translation vectors between different polytypes, we reveal how Form I and Form II are closely related. This microstructure is pervasive on the nanoscale to the extent that multiple forms may be present within a single sub-micron particle, as shown using 4D-STEM. With XRPD data we confirm the co-existence of these two polytypes, and we show that further stacking faults modelling is necessary to fit the data satisfactorily. We believe the methods and findings presented in this work extend beyond xanthine and related purines and apply to a much larger set of organic planar molecules. Via relatively strong supramolecular interactions, many of these small organic molecular crystals form layers held together by weak interactions, which makes them ideal candidates for stacking faults and polytypism. Furthermore, solid solutions doped with different molecules 66 could also exhibit similar behaviour.