The effect of caries in EPR dosimetry of tooth enamel (in the dose range of 0–1 Gy) was investigated. The enamel of each tooth was divided into carious, non-carious and intermediate portions. The EPR signals of enamel at g = 2.0018 (dosimetric) and g = 2.0045 (native) were examined. The intensity of the dosimetric signal was the same for all three portions, while that of the native signal was higher for carious portions than for non-carious and intermediate portions. Reconstruction of the laboratory applied doses was done using all portions. Reasonable correlation between nominal and reconstructed doses was found in most cases. The effect of alkali treatment on the native and dosimetric signals of enamel was also tested. Reduction of the native signal intensity, particularly in the carious portions, was found to be the only significant effect. This resulted in a slight improvement in the accuracy of the reconstructed doses.