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Diagnosis of infected and affected dentine is an important factor in clininal restorative treatment of dentine. In this study, the IR and Raman spectra of the sound dentine, infected dentine and affected dentine are reported. The structure of infected dentine and affected dentine has been compared with the sound dentine and hydroxyapatite. It is shown while the infected dentine has lost its structure, the affected dentine has more or less a structure similar to the sound dentine. The molecular structure of collagen remains unchanged in both infected and affected dentine.