The aim of the present work was to investigate how the native signal observed in the electron paramagnetic resonance (EPR) spectrum of tooth enamel and dentin is associated with the organic content of the two tissues. This was achieved by comparing the EPR native signal and the optical bands (Raman and infrared, IR) associated with organic components of tooth enamel and dentin, in natural and deproteinated samples. The main results were: (a) in natural samples, the organic optical bands are more intense in dentin than in enamel, in contrast with the EPR native signal which shows similar intensity in the two tissues; (b) after deproteination, the optical organic bands are completely suppressed in both dentin and enamel, while the EPR native signal is eliminated only in dentin. It is suggested that the IR and Raman organic bands are originated in the bulk of the organic matrix, while the paramagnetic centres associated with the EPR native signal are located in the organic-mineral interface.