In 2017, the National Museum commemorated the bicentenary of the discovery of the Manuscript of Dvůr Králové and the Manuscript of Zelená Hora by further material research into both works and especially by an exhibition of their originals. The main aims of this research into the manuscripts included the documentation and evaluation of their current physical condition and the mapping of the effect of the microchemical analyses performed in the context of the disputes over the authenticity of the manuscripts between the middle of the 19th century and the 1970s. For the achievement of these objectives, a detailed documentation of all the pages of the manuscripts in different types of lighting (visible direct, lateral, transmitted, ultraviolet, infrared), optical microscopy, and the identification of the degradation productions of damaged places by means of X-ray fluorescence analysis and Raman spectroscopy were used. This provided new information on the current physical condition of the manuscripts and documentation of the damage caused by historical microchemical testing. In addition, some previously unpublished historical tests were identified, thus offering a new perspective on some current damage of the two manuscripts.