During this study, chalices made about start of 17th century were investigated. This is the first time that these objects were studied from people outside the Abbey. The goal of the study was to characterize the gems of these items and to compare them with the observation of Father Eustach Tonassini at the end of 18th century. The examination of these chalices took place in the Laboratory for research in conservation at the Centre of collections of the Swiss national museum using only non-destructive methods. More precisely, binocular microscope on a modified stand was used to observe the internal features of the stones, long- and shortwave ultraviolet lamp to see their luminescence, x-ray fluorescence (XRF) for chemical and Raman spectrometer associated with a microscope for spectroscopic/vibration analysis. After the examination, it is found that all studied gems are natural; neither imitations nor synthetics were identified. It seems also, after studying pearls’ chemistry, that all are of saltwater origin. Moreover, comparing our results with those observed by Father Tonassini, it appears that what he had correctly all the rubies, except of some which are dark coloured almandines. He had correctly identified all diamonds too, amethysts (except of two which were dark coloured almandines), sapphires (except of one which is olivine) and emeralds (except for the big stones which are olivines). All the stones that he called “chrysolith” are olivines (the gems quality is a.k.a. peridot), these called “Hyakinths” grossulars and those called “Topaz” are either citrine or grossulars. Finally, Father Tonassini in his manuscript mentioned that the gems are “orientalisch”, i.e. from oriental countries. Studies of gems inclusions did not exclude this possibility. However, more research is needed in order to study better the possible geographical origin of these stones.