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The tree-ring stable C, O and H isotope compositions have proven valuable for examining past changes in the environment and predicting forest responses to environmental change. However, we have not yet recovered the full potential of this archive, partly due to a lack understanding of fractionation processes resulting from methodological constraints. With better understanding of the biochemical and tree physiological processes that lead to differences between the isotopic compositions of primary photosynthates and the isotopic compositions of substrates deposited in stem xylem, more reliable and accurate reconstructions could be obtained. Furthermore, by extending isotopic analysis of tree-ring cellulose to intra-molecular level, more information could be obtained on changing climate, tree metabolism or ecophysiology. This chapter presents newer methods in isotope research that have become available or show high future potential for fully utilising the wealth of information available in tree-rings. These include compound-specific analysis of sugars and cyclitols, high spatial resolution analysis of tree rings with UV-laser, and position-specific isotope analysis of cellulose. The aim is to provide the reader with understanding of the advantages and of the current challenges connected with the use of these methods for stable isotope tree-ring research.