Background: Illuminated manuscripts are complex multi-layer and multi-material objects. To this difficulty, from the analytical point of view, is added the impossibility of removing samples from these paintings for the study of their materials and techniques. There are relatively few analytical methods that satisfy these constraints as the availability of non-invasive techniques adapted to painted manuscripts is limited and mainly focused on the characterization of inorganic compounds. In the context of a research project on the analytical study of the forty miniatures in the Marcadé collection (Treasury of the Saint-André Cathedral of Bordeaux, XIII to XVI century), the potential of two non-invasive methods, hyperspectral imaging (HSI) and spectrofluorimetry is explored. Results: The methodological development of these techniques as well as preliminary tests on miniatures recreated according to medieval recipes and materials, allowed the validation of the analytical parameters and the creation of a database of reference spectra (parchments, pigments, binders). Hyperspectral imaging associates reflectance spectra with each pixel of the image and treats the signal received in various wavelengths. The characteristics of the spectral signal in VIS range or NIR are used to get an identification and a localization of the components. It allows the study of the entire image and offers lots of ways to work: comparison of spectra, mapping, principal component analyses and false color images. Spectrofluorimetry is a sensitive method which gives information on fluorescent organic compounds under UV or visible light. Emission and excitation spectra of five red pigments in binding media have been collected. These methods were compared with X-ray fluorescence spectrometry for the qualitative analysis and mapping of the inorganic elements in a facsimile which had been purposely reproduced by an illumination painter who worked with original medieval recipes for the sake of developing the present study. Conclusions: The combination of all these techniques allows good identification of all the materials used on an illuminated manuscript. The pertinent selection of the wavelengths used with the HSI system and a preliminary database and study of materials under UV and white light is described in this paper.