A study of the natural stone in the masonry of secular buildings – two palaces of Novgorodian archbishops from the 14th and 15th centuries – was made as part of the extensive archaeological and restoration work in the Novgorod Kremlin that began in 2006. The two structures are unique among mediaeval Novgorodian architecture of the 12th–15th centuries, other surviving examples of which are exclusively church buildings. The aim of the study was to determine whether the intended function of a building had on the particularities of the selection of types of stone and the choice of quarry sites. The main methods of study were laboratory analyses (thin section microscopy, X-ray fluorescence spectroscopy, electron microscopy and X-ray diffraction analysis). which showed that the durable, but hard to work, limestone used in the walls of the buildings was quarried for the most part from the Il'men Clint, 50 km from Novgorod on the other side of Lake Il'men. For paving floors, however, the builders used trimmed slabs of limestone obtained in a different place, possibly on the River Shelon’, 70 km from Novgorod or further afield. A comparison with other works of Novgorodian architecture from the 12th–15th centuries showed that this sort of differentiation between sources for building stone was established practice, as was the use of those particular quarry sites. In the course of this work, we developed a methodology for the identification of limestone that we recommend for use in further studies of the building stone used in Novgorodian architecture. The results obtained are proving important for the resolution of practical tasks in the restoration of Novgorod's architectural monuments.