The Manuscript of Dvůr Králové and the Manuscript of Zelená Hora are among the most famous and most discussed manuscripts from the collections of the National Museum. Both of them have been discussed mainly in terms of their authenticity, specifically the time when the texts recorded in them were written. In the past, both manuscripts were thus i.a. subjected to multiple chemical analyses, which have left their mark on their physical condition. This publication presents the results of the research whose aim was to document and evaluate the impact of the mentioned analyses. The research only used non-invasive imaging and analytical methods including photographs in different types of light, microscopic research, documentation by means of infrared reflectography and X-rays as well as the identification of pigments by X-ray fluorescence analysis and Raman spectroscopy.